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1. OprF Impacts Pseudomonas aeruginosa Biofilm Matrix eDNA Levels in a Nutrient-Dependent Manner

   https://doi.org/10.1128/jb.00080-23  

   Cassin, Erin K. ; Araujo-Hernandez, Sophia A. ; Baughn, Dena S. ; Londono, Melissa C. ; Rodriguez, Daniela Q. ; Al-Otaibi, Natalie S. ; Picard, Aude ; Bergeron, Julien R. ; Tseng, Boo Shan ( June 2023 , Journal of Bacteriology)

   O'Toole, George (Ed.)

   ABSTRACT The biofilm matrix is composed of exopolysaccharides, eDNA, membrane vesicles, and proteins. While proteomic analyses have identified numerous matrix proteins, their functions in the biofilm remain understudied compared to the other biofilm components. In the Pseudomonas aeruginosa biofilm, several studies have identified OprF as an abundant matrix protein and, more specifically, as a component of biofilm membrane vesicles. OprF is a major outer membrane porin of P. aeruginosa cells. However, current data describing the effects of OprF in the P. aeruginosa biofilm are limited. Here, we identify a nutrient-dependent effect of OprF in static biofilms, whereby Δ oprF cells form significantly less biofilm than wild type when grown in media containing glucose or low sodium chloride concentrations. Interestingly, this biofilm defect occurs during late static biofilm formation and is not dependent on the production of PQS, which is responsible for outer membrane vesicle production. Furthermore, while biofilms lacking OprF contain approximately 60% less total biomass than those of wild type, the number of cells in these two biofilms is equivalent. We demonstrate that P. aeruginosa Δ oprF biofilms with reduced biofilm biomass contain less eDNA than wild-type biofilms. These results suggest that the nutrient-dependent effect of OprF is involved in the maintenance of P. aeruginosa biofilms by retaining eDNA in the matrix. IMPORTANCE Many pathogens form biofilms, which are bacterial communities encased in an extracellular matrix that protects them against antibacterial treatments. The roles of several matrix components of the opportunistic pathogen Pseudomonas aeruginosa have been characterized. However, the effects of P. aeruginosa matrix proteins remain understudied and are untapped potential targets for antibiofilm treatments. Here, we describe a conditional effect of the abundant matrix protein OprF on late-stage P. aeruginosa biofilms. A Δ oprF strain formed significantly less biofilm in low sodium chloride or with glucose. Interestingly, the defective Δ oprF biofilms did not exhibit fewer resident cells but contained significantly less extracellular DNA (eDNA) than wild type. These results suggest that OprF is involved in matrix eDNA retention in biofilms. 

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2. Plastics select for distinct early colonizing microbial populations with reproducible traits across environmental gradients

   https://doi.org/10.1111/1462-2920.16391  

   Bos, Ryan P. ; Kaul, Drishti ; Zettler, Erik R. ; Hoffman, Jeffrey M. ; Dupont, Christopher L. ; Amaral‐Zettler, Linda A. ; Mincer, Tracy J. ( May 2023 , Environmental Microbiology)

   Little is known about early plastic biofilm assemblage dynamics and successional changes over time. By incubating virgin microplastics along oceanic transects and comparing adhered microbial communities with those of naturally occurring plastic litter at the same locations, we constructed gene catalogues to contrast the metabolic differences between early and mature biofilm communities. Early colonization incubations were reproducibly dominated by Alteromonadaceae and harboured significantly higher proportions of genes associated with adhesion, biofilm formation, chemotaxis, hydrocarbon degradation and motility. Comparative genomic analyses among the Alteromonadaceae metagenome assembled genomes (MAGs) highlighted the importance of the mannose‐sensitive hemagglutinin (MSHA) operon, recognized as a key factor for intestinal colonization, for early colonization of hydrophobic plastic surfaces. Synteny alignments of MSHA also demonstrated positive selection formshAalleles across all MAGs, suggesting thatmshAprovides a competitive advantage for surface colonization and nutrient acquisition. Large‐scale genomic characteristics of early colonizers varied little, despite environmental variability. Mature plastic biofilms were composed of predominantly Rhodobacteraceae and displayed significantly higher proportions of carbohydrate hydrolysis enzymes and genes for photosynthesis and secondary metabolism. Our metagenomic analyses provide insight into early biofilm formation on plastics in the ocean and how early colonizers self‐assemble, compared to mature, phylogenetically and metabolically diverse biofilms.

    

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3. Microbial Nitrogen Metabolism in Chloraminated Drinking Water Reservoirs

   https://doi.org/10.1128/mSphere.00274-20  

   Potgieter, Sarah C. ; Dai, Zihan ; Venter, Stephanus N. ; Sigudu, Makhosazana ; Pinto, Ameet J. ; McMahon, Katherine ( April 2020 , mSphere)

   ABSTRACT Ammonia availability due to chloramination can promote the growth of nitrifying organisms, which can deplete chloramine residuals and result in operational problems for drinking water utilities. In this study, we used a metagenomic approach to determine the identity and functional potential of microorganisms involved in nitrogen biotransformation within chloraminated drinking water reservoirs. Spatial changes in the nitrogen species included an increase in nitrate concentrations accompanied by a decrease in ammonium concentrations with increasing distance from the site of chloramination. This nitrifying activity was likely driven by canonical ammonia-oxidizing bacteria (i.e., Nitrosomonas ) and nitrite-oxidizing bacteria (i.e., Nitrospira ) as well as by complete-ammonia-oxidizing (i.e., comammox) Nitrospira -like bacteria. Functional annotation was used to evaluate genes associated with nitrogen metabolism, and the community gene catalogue contained mostly genes involved in nitrification, nitrate and nitrite reduction, and nitric oxide reduction. Furthermore, we assembled 47 high-quality metagenome-assembled genomes (MAGs) representing a highly diverse assemblage of bacteria. Of these, five MAGs showed high coverage across all samples, which included two Nitrosomonas, Nitrospira, Sphingomonas , and Rhizobiales -like MAGs. Systematic genome-level analyses of these MAGs in relation to nitrogen metabolism suggest that under ammonia-limited conditions, nitrate may be also reduced back to ammonia for assimilation. Alternatively, nitrate may be reduced to nitric oxide and may potentially play a role in regulating biofilm formation. Overall, this study provides insight into the microbial communities and their nitrogen metabolism and, together with the water chemistry data, improves our understanding of nitrogen biotransformation in chloraminated drinking water distribution systems. IMPORTANCE Chloramines are often used as a secondary disinfectant when free chlorine residuals are difficult to maintain. However, chloramination is often associated with the undesirable effect of nitrification, which results in operational problems for many drinking water utilities. The introduction of ammonia during chloramination provides a potential source of nitrogen either through the addition of excess ammonia or through chloramine decay. This promotes the growth of nitrifying microorganisms and provides a nitrogen source (i.e., nitrate) for the growth for other organisms. While the roles of canonical ammonia-oxidizing and nitrite-oxidizing bacteria in chloraminated drinking water systems have been extensively investigated, those studies have largely adopted a targeted gene-centered approach. Further, little is known about the potential long-term cooccurrence of complete-ammonia-oxidizing (i.e., comammox) bacteria and the potential metabolic synergies of nitrifying organisms with their heterotrophic counterparts that are capable of denitrification and nitrogen assimilation. This study leveraged data obtained for genome-resolved metagenomics over a time series to show that while nitrifying bacteria are dominant and likely to play a major role in nitrification, their cooccurrence with heterotrophic organisms suggests that nitric oxide production and nitrate reduction to ammonia may also occur in chloraminated drinking water systems. 

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4. Plasmid-Mediated Stabilization of Prophages

   https://doi.org/10.1128/msphere.00930-21  

   Tuttle, Matthew J. ; May, Frank S. ; Basso, Jonelle T. ; Gann, Eric R. ; Xu, Julie ; Buchan, Alison ( April 2022 , mSphere)

   McMahon, Katherine (Ed.)

   ABSTRACT Mobile genetic elements (MGEs) drive bacterial evolution, alter gene availability within microbial communities, and facilitate adaptation to ecological niches. In natural systems, bacteria simultaneously possess or encounter multiple MGEs, yet their combined influences on microbial communities are poorly understood. Here, we investigate interactions among MGEs in the marine bacterium Sulfitobacter pontiacus . Two related strains, CB-D and CB-A, each harbor a single prophage. These prophages share high sequence identity with one another and an integration site within the host genome, yet these strains exhibit differences in “spontaneous” prophage induction (SPI) and consequent fitness. To better understand mechanisms underlying variation in SPI between these lysogens, we closed their genomes, which revealed that in addition to harboring different prophage genotypes, CB-A lacks two of the four large, low-copy-number plasmids possessed by CB-D. To assess the relative roles of plasmid content versus prophage genotype on host physiology, a panel of derivative strains varying in MGE content were generated. Characterization of these derivatives revealed a robust link between plasmid content and SPI, regardless of prophage genotype. Strains possessing all four plasmids had undetectable phage in cell-free lysates, while strains lacking either one plasmid (pSpoCB-1) or a combination of two plasmids (pSpoCB-2 and pSpoCB-4) produced high (>10 5 PFU/mL) phage titers. Homologous plasmid sequences were identified in related bacteria, and plasmid and phage genes were found to be widespread in Tara Oceans metagenomic data sets. This suggests that plasmid-dependent stabilization of prophages may be commonplace throughout the oceans. IMPORTANCE The consequences of prophage induction on the physiology of microbial populations are varied and include enhanced biofilm formation, conferral of virulence, and increased opportunity for horizontal gene transfer. These traits lead to competitive advantages for lysogenized bacteria and influence bacterial lifestyles in a variety of niches. However, biological controls of “spontaneous” prophage induction, the initiation of phage replication and phage-mediated cell lysis without an overt stressor, are not well understood. In this study, we observed a novel interaction between plasmids and prophages in the marine bacterium Sulfitobacter pontiacus . We found that loss of one or more distinct plasmids—which we show carry genes ubiquitous in the world’s oceans—resulted in a marked increase in prophage induction within lysogenized strains. These results demonstrate cross talk between different mobile genetic elements and have implications for our understanding of the lysogenic-lytic switches of prophages found not only in marine environments, but throughout all ecosystems. 

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5. Multi-functional low-cost epoxy based nanocomposite corrosion resistant coatings

   Nawani, Pranav ; Gese, Natalie ( June 2017 , MegaRust 2017 Organized by the American Society of Naval Engineers)

   Corrosion is a significant global issue, resulting in high maintenance and repair costs. Long term structural integrity of metal and its products is directly dependent on its anti-corrosive properties. Surfaces exposed to marine environments are prone to microbial attachment followed by biofilm formation, resulting in bio-fouling. Hence coatings are used to protect the surfaces against corrosion and biofilm formation. Currently various organic coatings are used to protect metals and the cost of these coatings is directly dependent upon the cost of the fillers used to impart specific properties. Conventionally fillers such as zinc, Titanium and Silver based compounds are used in coatings for corrosion and/or microbial protection of surfaces, which are expensive. The underlying issue with using these compounds as fillers is that they can adversely effect mechanical and barrier properties, due to which they are used as a base coat and additional fillers are used to compensate for such property losses. Most of these coatings need an enhanced anti-microbial surface and improvement in their barrier efficacy against water/moisture, oxygen, and chloride ions. Hence it is imperative to develop low-cost fillers that will enhance both active & passive corrosion resistance properties, prevent microbial attachment on the surfaces and will not degrade any polymeric properties. In this work, ASL is developing a multi-functional low cost epoxy-clay nanocomposite coating, for microbial and corrosion resistance. Multi-functional coatings are developed using a multi-component approach, where the innovation lays in deriving the benefits of various fillers through a combinatorial approach to synergistic harvesting of functionality and vigor. The primary filler is a naturally abundant clay material and, owing to their sheet like morphology and layered structures, their surface can be modified to achieve the desired property enhancements. Sheet like morphology enhances polymer filler interactions, resulting in enhanced mechanical and reduced barrier properties. The presence of clay in the coating materials will mitigate the impact of moisture and chloride ions (in marine environment) providing passive protection to the coated surface. Modification of clay with transition metal ions (TMI) enhances corrosion resistance properties of coatings. 

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