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A direct viable count method for the enumeration of attached bacteria and assessment of biofilm disinfection

This report describes the adaptation of an in situ direct viable count (in situ DVC) method in biofilm disinfection studies. The results obtained with this technique were compared to two other enumeration methods, the plate count (PC) and conventional direct viable count (c-DVC). An environmental isolate (Klebsiella pneumoniae Kp1) was used to form biofilms on stainless steel coupons in a stirred batch reactor. The in situ DVC method was applied to directly assess the viability of bacteria in biofilms without disturbing the integrity of the interfacial community. As additional advantages, the results were observed after 4 h instead of the 24 h incubation time required for colony formation and total cell numbers that remained on the substratum were enumerated. Chlorine and monochloramine were used to determine the susceptibilities of attached and planktonic bacteria to disinfection treatment using this novel analytical approach. The planktonic cells in the reactor showed no significant change in susceptibility to disinfectants during the period of biofilm formation. In addition, the attached cells did not reveal any more resistance to disinfection than planktonic cells. The disinfection studies of young biofilms indicated that 0.25 mg/l free chlorine (at pH 7.2) and 1 mg/l monochloramine (at pH 9.0) have comparable disinfection efficiencies at 25 degrees C. Although being a weaker disinfectant, monochloramine was more effective in removing attached bacteria from the substratum than free chlorine. The in situ DVC method always showed at least one log higher viable cell densities than the PC method, suggesting that the in situ DVC method is more efficient in the enumeration of biofilm bacteria. The results also indicated that the in situ DVC method can provide more accurate information regarding the cell numbers and viability of bacteria within biofilms following disinfection.

NASA Discipline Number 04-10↗

A Preliminary Modeling Study of Biofilm Accumulation in the Water Recovery System

Bacterial biofilms are ubiquitous in wastewater systems on earth and in spacecraft, such as in the International Space Station (ISS) wastewater processing assembly (WPA), where they cause problems in the tank, solenoid valves, and pipelines. Downstream filter applications, tank cycling, and regular biocide water flushing have been used to control biofilm accumulation on board the ISS. Biofilm control is expected to be a challenge for long-term missions with a dormancy period of up to a year, as stagnant water systems are highly susceptible to biofilm growth. Flushing of the system with biocidal water has been proposed to avoid biomass problems for long-term missions. To validate the proposed flush method, a mathematical model, based on the metabolism maintenance rate of bacteria, is being developed to understand the current biofilm accumulation rate in the ISS WPA system and to calculate the biomass production rate under dormancy-like conditions. This method of quantification of biofilm can be applied as a function of nutrient inputs to guide the selection and optimization of biofilm mitigation approaches. The method can also be helpful in understanding, defining, quantifying, visualizing, and simulating the state of the water processing system during operation and after dormancy.

Angie M Diaz↗

Preparation for and Performance of a Pseudomonas aeruginosa Biofilm Experiment On Board the International Space Station

Biofilms are a problem on Earth given their ability to degrade the materials upon which they grow and due to their relevance to infections. Remarkably, 65% and 80% of infections and chronic diseases on Earth are associated with biofilms, respectively. In space, these problems' impact is higher because the crew's lives and mission success depend on nominal operation of mechanical systems. Furthermore, the isolated confined environment nature of spaceflight may increase the rates of disease transmission. In the case of the International Space Station (ISS), biofilms are an identified problem on the Environmental Control and Life Support System (ECLSS), namely on the water processor assembly (WPA). In late 2019, the Space Biofilms experiment launched towards ISS to (i) characterize the mass, thickness, morphology, and gene expression of biofilms formed in space with respect to matched Earth controls, (ii) interrogate the expression of antimicrobial resistance genes, and (iii) test novel materials as potential biofilm control strategies for future ECLSS components. For this, 288 bacterial samples were prepared prior to the launch of the Northrop Grumman CRS-12 mission from NASA's Wallops Flight Facility. The samples were integrated into the spaceflight hardware, BioServe's Fluid Processing Apparatus (FPA) packed in sets of eight in Group Activation Packs (GAP). Half of these samples were activated and terminated on orbit by NASA astronauts Jessica Meir and Christina Koch, while the remaining half were processed equivalently on Earth. The spaceflight bacterial samples of Space Biofilms returned on board SpaceX' CRS-19 Dragon spacecraft, in early 2020. We here describe the test campaign implemented to verify the experiment design and confirm it would enable us to achieve the project's scientific goals. This campaign ended with the Experiment Verification Test (EVT), from which we here present example morphology and transcriptomic results. We describe in detail the sample preparation prior to flight, including cleaning and sterilization of the coupons of six materials (SS316, passivated-SS316, lubricant impregnated surface, catheter-grade silicone with and without a nanotopography, and cellulose membrane), loading and integration of growth media, bacterial inoculum, fixative and preservative to enable experiment termination on orbit. Additionally, we describe the performance of the experiment on board the ISS, including crew activities, use of assets, temperature profile, and experiment timeline; all leading to a successful spaceflight experiment.

Pamela Flores↗

Potential Biofilm Control Strategies for Extended Spaceflight Missions

Biofilms, surface-adherent microbial communities, are associated with microbial fouling and corrosion in terrestrial water-distribution systems. Biofilms are also present in human spaceflight, particularly in the Water Recovery System (WRS) on the International Space Station (ISS). The WRS is comprised of the Urine Processor Assembly (UPA) and the Water Processor Assembly (WPA) which together recycles wastewater from human urine and recovered humidity from the ISS atmosphere. These wastewaters and various process streams are continually inoculated with microorganisms primarily arising from the space crew microbiome. Biofilm-related fouling has been encountered and addressed in spacecraft in low Earth orbit, including ISS and the Russian Mir Space Station. However, planned future missions beyond low Earth orbit to the Moon and Mars present additional challenges, as resupplying spare parts or support materials would be impractical and the mission timeline would be in the order of years in the case of a mission to Mars. In addition, future missions are expected to include a period of dormancy in which the WRS would be unused for an extended duration. The concepts developed in this review arose from a workshop including NASA personnel and representatives with biofilm expertise from a wide range of industrial and academic backgrounds. Here, we address current strategies that are employed on Earth for biofilm control, including antifouling coatings and biocides and mechanisms for mitigating biofilm growth and damage. These ideas are presented in the context of their applicability to spaceflight and identify proposed new topics of biofilm control that need to be addressed in order to facilitate future extended, crewed, spaceflight missions.

Luis Zea↗

Boric Acid Dispersion of Biofilm (BAD-B)

Biofilms in spacecraft water recycling systems (WRS) can cause crew illness, occlude water lines, and induce corrosion on WRS materials. The treatment of biofilms in spacecraft water systems has historically been limited by a lack of suitable methods to overcome biofilm-associated antimicrobial tolerance (AMT). One way to get around AMT is to induce biofilm dispersion. To address AMT in spacecraft WRS, I evaluated the use of boric acid (BA) as an agent to disperse biofilms formed on common WRS materials, including 316L stainless steel, PFTE Teflon, and Ti6Al4V titanium alloy. Recent studies have shown that BA can be effective at dispersing biofilms of a variety of bacterial species. BA has also been shown to interact synergistically with antibiotics and disinfectants.

microbiology↗

ToF-SIMS spectral data analysis of Paenibacillus sp. 300A biofilms and planktonic cells

Analysis of bacterial biofilms is particularly challenging and important with diverse applications from systems biology to biotechnology. Among the variety of techniques that have been applied, time-of-flight secondary ion mass spectrometry (ToF-SIMS) has many promising features in studying the surface characteristics of biofilms. ToF-SIMS offers high spatial resolution and high mass accuracy, which permit surface sensitive analysis of biofilm components. Thus, ToF-SIMS provides a powerful solution to addressing the challenge of bacterial biofilm analysis. This dataset covers ToF-SIMS analysis of Paenibacillus sp. 300A (300A) isolated from the Hanford site in Richland, WA. The strain is known to have metal and sulfur reducing properties and can be used for bioremediation, wastewater treatment, bioengineering and technology development. There is a current need to identify small molecules and fragments produced from bacterial biofilms. Static ToF-SIMS spectra of 300A were obtained using an IONTOF TOF-SIMS V instrument equipped with a 25 keV Bi 3 + metal ion gun. Identified molecules and molecular fragments are compared against known biological databases and the reported peaks have at least 65 ppm mass accuracy. These molecules range from lipids and fatty acids to flavonoids, quinolones, and other naturally occurring organic compounds. It is anticipated that the spectral identification of key peaks will assist detection of metabolites, extracellular polymeric substance molecules like polysaccharides, and biologically relevant small molecules using ToF-SIMS in future surface and interface research of bacterial biofilms.

Biofilms↗

Rheinheimera sp . T2C2 Bacterial Biofilm for Bioremediation of Cobalt(II)

Toxic metals, including cobalt, are often the cause of the contamination of rivers and lakes in mining regions. Heavy metal water pollution has been linked to numerous human health problems, prompting the need for environmental remediation. Existing techniques for removing heavy metals from water, such as chemical precipitation and filtration, produce toxic waste, are costly, or require high power consumption for pumping. Biosorption is a potential alternative strategy that is cost-effective and uses readily available and naturally produced biomass and living material to absorb pollutants. Engineering living materials, such as biofilms, which consist of living cells and a secreted polymer matrix, offer the potential to integrate toxin sensing, sequestration, and metabolism capabilities of cells to improve pollution remediation strategies. Alternative biofilm producing candidates need to be explored to implement these material capabilities. Previous biosorption studies have primarily used bacterial biofilms from known pathogens and/or generated toxic waste in the form of the absorbent material combined with the heavy metal. Here, we describe a recently isolated bacterium called Rheinheimera sp. T2C2 that forms biofilms with promising biosorption characteristics. T2C2 is an aquatic bacterium with low nutrient requirements and high biofilm production that is not known to be pathogenic. We demonstrate (1) the efficacy of Rheinheimera sp. T2C2 as a biosorbent for cobalt bioremediation; (2) how biosorption is altered by water conditions to establish the efficacy of this strategy in different environments; and (3) how the metal can be released from the biofilm for metal recycling. Our findings will provide a living materials strategy that overcomes the existing barriers for bioremediation and improves the health of ecosystems and humans through heavy metal removal and recycling.

Rheinheimera↗

Extensive cellular multi-tasking within Bacillus subtilis biofilms

Bacillus subtilis is a soil-dwelling bacterium that can form biofilms, or communities of cells surrounded by a self-produced extracellular matrix. In biofilms, genetically identical cells often exhibit heterogeneous transcriptional phenotypes, so that subpopulations of cells carry out essential yet costly cellular processes that allow the entire population to thrive. Surprisingly, the extent of phenotypic heterogeneity and the relationships between subpopulations of cells within biofilms of even in well-studied bacterial systems like B. subtilis remains largely unknown. To determine relationships between these subpopulations of cells, we created 182 strains containing pairwise combinations of fluorescent transcriptional reporters for the expression state of 14 different genes associated with potential cellular subpopulations. We determined the spatial organization of the expression of these genes within biofilms using confocal microscopy, which revealed that many reporters localized to distinct areas of the biofilm, some of which were co-localized. We used flow cytometry to quantify reporter co-expression, which revealed that many cells “multi-task,” simultaneously expressing two reporters. These data indicate that prior models describing B. subtilis cells as differentiating into specific cell types, each with a specific task or function, were oversimplified. Only a few subpopulations of cells, including surfactin and plipastatin producers, as well as sporulating and competent cells, appear to have distinct roles based on the set of genes examined here. These data will provide us with a framework with which to further study and make predictions about the roles of diverse cellular phenotypes in B. subtilis biofilms.

59 BASIC BIOLOGICAL SCIENCES↗

Protection and enrichment: how two different carbonaceous biofilm supports improve methane yield from encapsulated anaerobic microorganisms

Encapsulating anaerobic microorganisms allows for the separation of the solids retention time from the hydraulic retention time during anaerobic wastewater treatment. The harsh chemistries involved in the process of encapsulation can have adverse effects on microorganisms for anaerobic digestion, especially methanogens, and can lead to lower methane yields after encapsulation. Improving the survival and maintaining activity of anaerobic communities during encapsulation will likely be the key to improving methane yield. In this study, we investigated the encapsulation of biomass grown as biofilms on two carbonaceous materials, biochar and powdered activated carbon (PAC), to improve methane yield. Microorganisms grown as biofilms on biochar and PAC were encapsulated in polyethylene glycol (PEG) and incubated for 10 days. After 10 days, the unamended control capsules produced 81.6 ± 5.4 μmol of methane, while PAC-amended capsules produced 129.8 ± 1.9 μmol and biochar-amended capsules produced 432.96 ± 20.8 μmol methane, with the differences being statistically significant (p < 0.05). In biochar, a higher relative abundance of methanogens led to increased methane production capacity. The ratio of the methyl coenzyme M reductase (mcrA) genes to total 16S rRNA genes in the encapsulated biochar-supported biofilms was significantly higher than that in the encapsulated unsupported (p = 4.9 × 10 −5 ) and the PAC-supported biofilms (p = 0.012). Biochar-supported biofilms also had higher methane output per mcrA or 16S rRNA gene copy number. For the PAC, biofilms were protected from ammonium persulfate (APS), a powerful oxidant used in the encapsulation process. PAC removed 92% of dissolved APS, reducing exposure of the methanogens to this chemical. Unfortunately, this removal of APS compromised capsule stability, limiting the amount of PAC that could be added to the capsules. Furthermore, amendments that improve survival and activity of methanogens should be used in the capsules instead of those that protect methanogens by interfering with encapsulant polymerization chemistry.

Resource recovery↗

The ability of Salmonella enterica subsp. enterica strains to form biofilms on abiotic surfaces and their susceptibility to selected essential oil components

Abstract The ability of Salmonella enterica subsp. enterica to persist and form biofilms on different surfaces can constitute a source of food contamination, being an issue of global concern. The objective of this study was to understand the biofilm formation profile of 14 S. enterica strains among different serovars and sources and to evaluate the ability of essential oil (EO) components (carveol, citronellol, and citronellal) to disinfect the biofilms formed on stainless steel and polypropylene surfaces. All the strains were able to form biofilms with counts between 5.34 to 6.78 log CFU cm−2. Then, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of EO components were evaluated on two selected strains. All compounds inhibited the growth of Salmonella Typhimurium (strain 1; MIC = 800–1000 µg ml−1) and Salmonella Enteritidis (strain 5; MIC = 400–1000 µg ml−1) and only carveol showed bactericidal activity against strains 1 and 5 (MBC = 1200 µg ml−1). Biofilms were exposed to the EO components at 10 × MIC for 30 min and polypropylene surfaces were more difficult to disinfect showing reductions between 0.9 and <1.2 log CFU cm−2. In general, the S. enterica biofilms demonstrated a significant tolerance to disinfection, demonstrating their high degree of recalcitrance on food processing surfaces.

Pérez-Lavalle, Liliana (ORCID:0000000344825031)↗

Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism

Abstract Background Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs to investigate microbial controls on biogeochemical cycling. Results Sulfide springs biofilms were investigated using bulk geochemical analysis, genome-resolved metagenomics, and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix and Beggiatoa , dominate the biofilms, which also contain CPR Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, and Parcubacteria. STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts. STXM and NEXAFS spectroscopy at carbon K and sulfur L 2,3 edges show that filamentous bacteria contain protein-encapsulated spherical elemental sulfur granules, indicating that they are sulfur oxidizers, likely Thiothrix . Berkelbacteria and Moranbacteria in the same biofilm sample are predicted to have a novel electron bifurcating group 3b [NiFe]-hydrogenase, putatively a sulfhydrogenase, potentially linked to sulfur metabolism via redox cofactors. This complex could potentially contribute to symbioses, for example, with sulfur-oxidizing bacteria such as Thiothrix that is based on cryptic sulfur cycling. One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that may convert thiosulfate to sulfite. We find similar conserved genomic architecture associated with CPR bacteria from other sulfur-rich subsurface ecosystems. Conclusions Our combined metagenomic, geochemical, spectromicroscopic, and structural bioinformatics analyses of biofilms growing in sulfide-rich springs revealed consortia that contain CPR bacteria and sulfur-oxidizing Proteobacteria, including Thiothrix , and bacteria from a new family within Beggiatoales. We infer roles for CPR bacteria in sulfur and hydrogen cycling.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization of Oral Candida spp. Biofilms in Children and Adults Carriers from Eastern Europe and South America

Background: Candida albicans and non-Candida albicans Candida species (NCACs) are known to colonize and invade various tissues, including the oral mucosa. In this work, we aimed to characterize mature biofilms of several Candida spp. clinical isolates (n = 33) obtained from the oral mucosa of children, adults, and elders of Eastern Europe and South America. Methods: Each strain was evaluated for its capacity to form biofilms in terms of total biomass using the crystal violet assay and for matrix components production (proteins and carbohydrates) using the BCA and phenol-sulfuric tests, respectively. The effect of different antifungals on biofilm formation was studied. Results: in the children’s group, a predominance of C. krusei (81%) was observed, while, among adults, the main species was C. albicans (59%). Most strains showed a reduced response to antimicrobial drugs when in biofilm form (p < 0.01). Moreover, it was observed that strains isolated from children produced more matrix, with higher levels of protein and polysaccharides. Conclusions: children were more likely to be infected by NCACs than adults. More importantly, these NCACs were able to form biofilms richer in matrix components. This finding is of clinical importance, particularly in pediatric care, since stronger biofilms are highly associated with antimicrobial resistance, recurrent infections, and higher therapeutic failure.

Alves, Anelise Maria Costa Vasconcelos (ORCID:0000↗

Microbial biofilm studies of the environmental control and life support system water recovery test for Space Station Freedom

NASA is developing a water recovery system (WRS) for Space Station Freedom to reclaim human waste water for reuse by astronauts as hygiene or potable water. A water recovery test (WRT) currently in progress investigates the performance of a prototype of the WRS. Analysis of biofilm accumulation, the potential for microbially influenced corrosion (MIC) in the WRT, and studies of iodine disinfection of biofilm are reported. Analysis of WRT components indicated the presence of organic deposits and biofilms in selected tubing. Water samples for the WRT contained acid-producing and sulfate-reducing organisms implicated in corrosion processes. Corrosion of an aluminum alloy was accelerated in the presence of these water samples; however, stainless steel corrosion rates were not accelerated. Biofilm iodine sensitivity tests using an experimental laboratory scale recycled water system containing a microbial check valve (MCV) demonstrated that an iodine concentration of 1 to 2 mg/L was ineffective in eliminating microbial biofilm. For complete disinfection, an initial concentration of 16 mg/L was required, which was gradually reduced by the MCV over 4 to 8 hours to 1 to 2 mg/L. This treatment may be useful in controlling biofilm formation.

Rodgers, E. B.↗

Aquatic biofilms and their responses to disinfection and invading species

The control of microbial contamination is a primary concern in the development of a water reclamation system for long-duration manned space flights. This paper describes bench-scale experiments, using both static and recycling water systems, investigating the interaction of bacterial species in the development of a biofilm and their response to the introduction of a disinfectant or of additional species. The results showed that iodine concentrations as high as 15 to 20 mg/l I2 are necessary to completely disinfect a stable biofilm. When S. aueus and E. coli were introduced into a system containing natural mixed culture biofilms, their colonization in the biofilms increased their survival time, from 3 to 5 days as unattached cells to over 60 days when protected in the biofilms. While iodine concentrations of 0.5 to 1 mg/l were enough to eliminate these organisms from the bulk water, concentrations higher than 4.0 mg/l were necessary to completely eliminate these organisms from the biofilm.

Smithers, G. A.↗

Tetracycline rapidly reaches all the constituent cells of uropathogenic Escherichia coli biofilms

We have developed a method for visualizing Escherichia coli cells that are exposed to tetracycline in a biofilm, based on a previous report that liposomes containing the E. coli TetR(B) protein fluoresce when exposed to this antibiotic. By our method, cells devoid of TetR(B) also exhibited tetracycline-dependent fluorescence. At 50 microg of tetracycline ml(-1), planktonic cells of a uropathogenic E. coli (UPEC) strain developed maximal fluorescence after 7.5 to 10 min of exposure. A similar behavior was exhibited by cells in a 24- or 48-h UPEC biofilm, as examined by confocal laser microscopy, regardless of whether they lined empty spaces or occupied densely packed regions. Further, a comparison of phase-contrast and fluorescent images of corresponding biofilm zones showed that all the cells fluoresced. Thus, all the biofilm cells were exposed to tetracycline and there were no pockets within the biofilm where the antibiotic failed to reach. It also appeared unlikely that niches of reduced exposure to the antibiotic existed within the biofilms.

Non-NASA Center↗

Ultraviolet-Absorption Spectroscopic Biofilm Monitor

An ultraviolet-absorption spectrometer system has been developed as a prototype instrument to be used in continuous, real-time monitoring to detect the growth of biofilms. Such monitoring is desirable because biofilms are often harmful. For example, biofilms in potable-water and hydroponic systems act as both sources of pathogenic bacteria that resist biocides and as a mechanism for deterioration (including corrosion) of pipes. Biofilms formed from several types of hazardous bacteria can thrive in both plant-growth solutions and low-nutrient media like distilled water. Biofilms can also form in condensate tanks in air-conditioning systems and in industrial heat exchangers. At present, bacteria in potable-water and plant-growth systems aboard the space shuttle (and previously on the Mir space station) are monitored by culture-plate counting, which entails an incubation period of 24 to 48 hours for each sample. At present, there are no commercially available instruments for continuous monitoring of biofilms in terrestrial or spaceborne settings.

Micheels, Ronald H.↗

Hyperspectral Biofilm Classification Analysis for Carrying Capacity of Migratory Birds in the South Bay Salt Ponds

Tidal marshes are highly productive ecosystems that support migratory birds as roosting and over-wintering habitats on the Pacific Flyway. Microphytobenthos, or more commonly 'biofilms' contribute significantly to the primary productivity of wetland ecosystems, and provide a substantial food source for macroinvertebrates and avian communities. In this study, biofilms were characterized based on taxonomic classification, density differences, and spectral signatures. These techniques were then applied to remotely sensed images to map biofilm densities and distributions in the South Bay Salt Ponds and predict the carrying capacity of these newly restored ponds for migratory birds. The GER-1500 spectroradiometer was used to obtain in situ spectral signatures for each density-class of biofilm. The spectral variation and taxonomic classification between high, medium, and low density biofilm cover types was mapped using in-situ spectral measurements and classification of EO-1 Hyperion and Landsat TM 5 images. Biofilm samples were also collected in the field to perform laboratory analyses including chlorophyll-a, taxonomic classification, and energy content. Comparison of the spectral signatures between the three density groups shows distinct variations useful for classification. Also, analysis of chlorophyll-a concentrations show statistically significant differences between each density group, using the Tukey-Kramer test at an alpha level of 0.05. The potential carrying capacity in South Bay Salt Ponds is estimated to be 250,000 birds.

Hsu, Wei-Chen↗

Mitigation and Use of Biofilms in Space for the Benefit of Human Space Exploration

Biofilms are groups of cells of the same or different species living in communities. Such structures are usually attached to surfaces, and on Earth, they have been found in diverse and extreme environments. Such agglomerations have been described as recalcitrant or protective when facing adversity. In space systems, biofilms have been found on a multitude of hardware surfaces. Different studies have identified genetic changes that may impact human health. The insufficiency of consistent research may return inconclusive arguments as to what extent microgravity encourages virulence and how biofilms could exacerbate crewed spaceflight–especially ones to remote areas with a lack of resupply and service missions. However, biofilms are also beneficial to plant biology, and they may supply in metabolic pathways that produce useful organic and inorganic components to maintain life in other celestial bodies. There are expansive areas of research that look into biofilms in space and scientific recommendations that reflect on expanding the aerospace industry’s knowledge of biofilms, how to mitigate, or use them to the advantage of spaceflight.

Yo-ann Velez Justiniano↗