Thickness determines microbial community structure and function in nitrifying biofilms via deterministic assembly

Biochar coupled with multiple technologies for the removal of nitrogen and phosphorus from water: A review

Water eutrophication caused by nitrogen (N) and phosphorus (P) has become a global environmental issue. Biochar is a competent adsorbent for removing N and P from wastewater. However, compared with commercial activated carbon, biochar has relatively limited adsorption capacity. To broaden the field scale application of biochar, biochar coupled with multiple technologies (BC-MTs) (such as microorganisms, electrochemistry, biofilm, phytoremediation, etc.) have been extensively developed for environmental remediation. Nevertheless, due to the fluctuations and differences in biochar types, coupling methods, and wastewater types, various techniques show different removal mechanisms and performance, hindering the promotion and application of BC-MTs. A systematic review of the research progress of BC-MTs is highly necessary to gain a better understanding of the current research status and progress, as well as to promote the application of these techniques. In this paper, the application of pristine and modified biochar in adsorbing N and P in wastewater is critically reviewed. Then the removal performance, influencing factors, mechanisms, and the environmental applications of BC-MTs in wastewater are systematically summarized. In addition, the cost analysis and risk assessment of BC-MTs in environmental applications are conducted. Finally, suggestions and prospects for future research and practical application are put forward.

Biofilm inhibition of denture cleaning tablets and carvacrol on denture bases produced with different techniques

OBJECTIVES

This study compares the biofilm inhibition effects of denture cleaning tablets, carvacrol, and their combined use against Candida albicans on denture bases produced with different techniques. Additionally, the surface roughness and contact angles of these denture bases were evaluated.

MATERIALS AND METHODS

Test samples were prepared from four different denture base materials (cold-polymerized, heat-polymerized, CAD/CAM milling, and 3D-printed). The surface roughness and contact angles of the test samples were measured using a profilometer and goniometer, respectively. For the evaluation of biofilm inhibition, samples were divided into 5 subgroups: Corega and carvacrol, separately and combined treatments, positive (inoculated with C. albicans) and negative control (non-inoculated with C. albicans, only medium). Biofilm mass was determined using the crystal violet method. An additional prepared test sample for each subgroup was examined under scanning electron microscopy (SEM).

RESULTS

The surface roughness values of the 3D-printed test samples were found to be statistically higher than the other groups (P < .001). The water contact angle of all test materials was not statistically different from each other (P > .001). Corega and carvacrol, separately and combined, significantly decreased the amount of biofilm on all surfaces (P < .0001). Treatment of corega alone and in combination with carvacrol to the 3D-printed material caused less C. albicans inhibition than the other groups (P < .001; P < .05).

CONCLUSIONS

The surface roughness values of all test groups were within the clinically acceptable threshold. Although Corega and carvacrol inhibited C. albicans biofilms, their combined use did not show a synergistic effect.

CLINICAL RELEVANCE

Carvacrol may be used as one of the disinfectant agents for denture cleaning due to its biofilm inhibition property.

Space biofilms - An overview of the morphology of Pseudomonas aeruginosa biofilms grown on silicone and cellulose membranes on board the international space station

Microorganisms' natural ability to live as organized multicellular communities - also known as biofilms - provides them with unique survival advantages. For instance, bacterial biofilms are protected against environmental stresses thanks to their extracellular matrix, which could contribute to persistent infections after treatment with antibiotics. Bacterial biofilms are also capable of strongly attaching to surfaces, where their metabolic by-products could lead to surface material degradation. Furthermore, microgravity can alter biofilm behavior in unexpected ways, making the presence of biofilms in space a risk for both astronauts and spaceflight hardware. Despite the efforts to eliminate microorganism contamination from spacecraft surfaces, it is impossible to prevent human-associated bacteria from eventually establishing biofilm surface colonization. Nevertheless, by understanding the changes that bacterial biofilms undergo in microgravity, it is possible to identify key differences and pathways that could be targeted to significantly reduce biofilm formation. The bacterial component of Space Biofilms project, performed on the International Space Station in early 2020, contributes to such understanding by characterizing the morphology and gene expression of bacterial biofilms formed in microgravity with respect to ground controls. Pseudomonas aeruginosa was used as model organism due to its relevance in biofilm studies and its ability to cause urinary tract infections as an opportunistic pathogen. Biofilm formation was characterized at one, two, and three days of incubation (37 °C) over six different materials. Materials reported in this manuscript include catheter grade silicone, selected due to its medical relevance in hospital acquired infections, catheter grade silicone with ultrashort pulsed direct laser interference patterning, included to test microtopographies as a potential biofilm control strategy, and cellulose membrane to replicate the column and canopy structure previously reported from a microgravity study. We here present an overview of the biofilm morphology, including 3D images of the biofilms to represent the distinctive morphology observed in each material tested, and some of the key differences in biofilm thickness, mass, and surface area coverage. We also present the impact of the surface microtopography in biofilm formation across materials, incubation time, and gravitational conditions. The Space Biofilms project (bacterial side) is supported by the National Aeronautics and Space Administration under Grant No. 80NSSC17K0036 and 80NSSC21K1950.

Biofilm colonization and succession in a full-scale partial nitritation-anammox moving bed biofilm reactor

BACKGROUND

Partial nitritation-anammox (PNA) is a biological nitrogen removal process commonly used in wastewater treatment plants for the treatment of warm and nitrogen-rich sludge liquor from anaerobic digestion, often referred to as sidestream wastewater. In these systems, biofilms are frequently used to retain biomass with aerobic ammonia-oxidizing bacteria (AOB) and anammox bacteria, which together convert ammonium to nitrogen gas. Little is known about how these biofilm communities develop, and whether knowledge about the assembly of biofilms in natural communities can be applied to PNA biofilms.

RESULTS

We followed the start-up of a full-scale PNA moving bed biofilm reactor for 175 days using shotgun metagenomics. Environmental filtering likely restricted initial biofilm colonization, resulting in low phylogenetic diversity, with the initial microbial community comprised mainly of Proteobacteria. Facilitative priority effects allowed further biofilm colonization, with the growth of initial aerobic colonizers promoting the arrival and growth of anaerobic taxa like methanogens and anammox bacteria. Among the early colonizers were known 'oligotrophic' ammonia oxidizers including comammox Nitrospira and Nitrosomonas cluster 6a AOB. Increasing the nitrogen load in the bioreactor allowed colonization by 'copiotrophic' Nitrosomonas cluster 7 AOB and resulted in the exclusion of the initial ammonia- and nitrite oxidizers.

CONCLUSIONS

We show that complex dynamic processes occur in PNA microbial communities before a stable bioreactor process is achieved. The results of this study not only contribute to our knowledge about biofilm assembly and PNA bioreactor start-up but could also help guide strategies for the successful implementation of PNA bioreactors. Video Abstract.

Impacts of substrate properties and aquatic nutrient concentrations on the relative abundance of nitrifying/denitrifying genes and the associated microbes in epilithic biofilms

Substrates like sand or gravels and aquatic nutrient concentrations of rivers are highly heterogeneous, influencing the abundance of functional genes in epilithic biofilms where nitrification-denitrification processes take place. To analyze how the relative abundance of nitrifying/denitrifying genes and the associated microbes changes with the physical properties of substrates and aquatic concentrations of nutrients, this paper utilized metagenomics to comprehensively characterize these functional genes (i.e., amoA, hao, and nxrB involved in nitrification, and napA, narG, nirS, norB, and nosZ associated with denitrification) from epilithic biofilms collected along the Shitingjiang River in Southwest China and further obtained the relative abundance of major nitrifiers and denitrifiers. The results show that substrate size most significantly affects the relative abundance of hao and norB by altering the hydrodynamic conditions. In sampling sites with high heterogeneity in substrate size distribution, the relative abundance of most denitrifying genes is also higher. The carbon-nitrogen ratio negatively correlates with the relative abundance of all the nitrifying genes, while ammonium, total inorganic carbon, and total organic carbon concentrations positively affect the relative abundance of amoA and nxrB. As to the relative abundance of nitrifiers and denitrifiers, mainly belonging to phyla Proteobacteria and Actinobacteria, substrate heterogeneity and the aquatic concentrations of nutrients have greater influences than substrate size. Also, the substrate heterogeneity exerted positive influence on functional species of Pseudogemmobacter bohemicus and Paracoccus zhejiangensis. Considering the genes' functions and the dominant species linked to denitrification, nitrous oxide is more likely to occur in rivers with higher heterogeneity and larger substrates.

Effect of biofilm thickness on the activity and community composition of phosphorus accumulating bacteria in a moving bed biofilm reactor

Can biofilms enhance the rates of phosphorus removal in wastewater treatment? In order to narrow the scientific gap on the effect of biofilm thickness on the activity and microbial community of phosphorus-accumulating bacteria, this study investigated biofilms of 30 to 1000 µm thickness in a moving bed biofilm reactor. Measurements on 5 different biofilm carriers showed that biomass-specific phosphorus release and uptake rates increased as a function of biofilm thickness for biofilms thinner than about 110 µm but were lower for thicker biofilms of about 550-1000 µm. The reduced phosphorus uptake and release rates in the thickest biofilms can result from substrate mass transfer limitations whereas the low activity in the thinnest biofilms can be related to a too high turnover rate in the biofilm due to heterotrophic growth. Additionally, the microbial ecology of the different biofilms confirms the observed phosphorus uptake and release rates. The results from the full-length 16S rRNA gene sequencing of the bacterial community showed that the thicker biofilms were characterized by higher relative abundance (40-58%) of potential phosphorus accumulating genera Zoogloea, Acinetobacter, Dechloromonas and Ca. Accumulibacter. In contrast, the thinner biofilms were dominated by the genus Ferribacterium (34-60%), which might be competing with phosphorus-accumulating bacteria as indicated by the relatively high acetate uptake rates in the thinner biofilms. It is concluded that there is an optimal biofilm thickness of 100-500 µm, at which the phosphorus accumulating bacteria have the highest activity.

Microfluidic investigation of the impacts of flow fluctuations on the development of Pseudomonas putida biofilms

Biofilms play critical roles in wastewater treatment, bioremediation, and medical-device-related infections. Understanding the dynamics of biofilm formation and growth is essential for controlling and exploiting their properties. However, the majority of current studies have focused on the impact of steady flows on biofilm growth, while flow fluctuations are common in natural and engineered systems such as water pipes and blood vessels. Here, we reveal the effects of flow fluctuations on the development of Pseudomonas putida biofilms through systematic microfluidic experiments and the development of a theoretical model. Our experimental results showed that biofilm growth under fluctuating flow conditions followed three phases: lag, exponential, and fluctuation phases. In contrast, biofilm growth under steady-flow conditions followed four phases: lag, exponential, stationary, and decline phases. Furthermore, we demonstrated that low-frequency flow fluctuations promoted biofilm growth, while high-frequency fluctuations inhibited its development. We attributed the contradictory impacts of flow fluctuations on biofilm growth to the adjustment time (T0) needed for biofilm to grow after the shear stress changed from high to low. Furthermore, we developed a theoretical model that explains the observed biofilm growth under fluctuating flow conditions. Our insights into the mechanisms underlying biofilm development under fluctuating flows can inform the design of strategies to control biofilm formation in diverse natural and engineered systems.

Mapping the microbial diversity associated with different geochemical regimes in the shallow-water hydrothermal vents of the Aeolian archipelago, Italy

Shallow-water hydrothermal vents are unique marine environments ubiquitous along the coast of volcanically active regions of the planet. In contrast to their deep-sea counterparts, primary production at shallow-water vents relies on both photoautotrophy and chemoautotrophy. Such processes are supported by a range of geochemical regimes driven by different geological settings. The Aeolian archipelago, located in the southern Tyrrhenian sea, is characterized by intense hydrothermal activity and harbors some of the best sampled shallow-water vents of the Mediterranean Sea. Despite this, the correlation between microbial diversity, geochemical regimes and geological settings of the different volcanic islands of the archipelago is largely unknown. Here, we report the microbial diversity associated with six distinct shallow-water hydrothermal vents of the Aeolian Islands using a combination of 16S rRNA amplicon sequencing along with physicochemical and geochemical measurements. Samples were collected from biofilms, fluids and sediments from shallow vents on the islands of Lipari, Panarea, Salina, and Vulcano. Two new shallow vent locations are described here for the first time. Our results show the presence of diverse microbial communities consistent in their composition with the local geochemical regimes. The shallow water vents of the Aeolian Islands harbor highly diverse microbial community and should be included in future conservation efforts.

Anammox-Mediated Hydroxyapatite Granules: Physicochemical Properties, 3D Hierarchy, and Biofilm Thickness

Biomineralization inspired the development of simultaneous biological transformations and chemical precipitation for simultaneous nitrogen removal and phosphorus recovery from wastewater, which could compensate for the incapacity of phosphorus management in the new biological route of anaerobic ammonium oxidation (anammox). In this study, we strengthened anammox-mediated biomineralization by long-term feeding of concentrated N, P, and Ca substrates, and a self-assembled matrix of anammox bacteria and hydroxyapatite (HAP) was fabricated in a granular shape, defined as HAP-anammox granules. HAP was identified as the dominant mineral using elemental analysis, X-ray diffraction, and Raman spectroscopy. The intensive precipitation of HAP resulted in a higher inorganic fraction and substantially improved settleability of anammox biomass, which facilitated HAP precipitation by acting as nucleation and metabolically elevated pH. By using X-ray microcomputed tomography, we visually represented the hybrid texture of interwoven HAP pellets and biomass, the core-shell layered architecture of different-sized HAP-anammox granules, and their homogeneously regulated thickness of the outer biofilm (from 118 to 635 μm). This unique architecture endows HAP-anammox granules with outstanding settleability, active biofilm, and tightly bonded biofilm with the carrier, which may explain the excellent performance of these HAP-anammox granules under various challenging operational conditions in previous studies.

Microfluidics for Biofilm Studies

Biofilms are multicellular communities held together by a self-produced extracellular matrix and exhibit a set of properties that distinguish them from free-living bacteria. Biofilms are exposed to a variety of mechanical and chemical cues resulting from fluid motion and mass transport. Microfluidics provides the precise control of hydrodynamic and physicochemical microenvironments to study biofilms in general. In this review, we summarize the recent progress made in microfluidics-based biofilm research, including understanding the mechanism of bacterial adhesion and biofilm development, assessment of antifouling and antimicrobial properties, development of advanced in vitro infection models, and advancement in methods to characterize biofilms. Finally, we provide a perspective on the future direction of microfluidics-assisted biofilm research.

Surface properties and initial bacterial biofilm growth on 3D-printed oral appliances: a comparative in vitro study

OBJECTIVES

To investigate the initial bacterial adhesion on 3D-printed splint materials in relation to their surface properties.

MATERIALS AND METHODS

Specimens of five printable splint resins (SHERAprint-ortho plus UV, NextDent Ortho Rigid, LuxaPrint Ortho Plus, V-Print Splint, KeySplint Soft), one polymethylmethacrylate (PMMA) block for subtractive manufacturing (Astron CLEARsplint Disc), two conventional powder/liquid PMMA materials (FuturaGen, Astron CLEARsplint), and one polyethylene terephthalate glycol (PETG) thermoplastic sheet for vacuum forming (Erkodur Thermoforming Foil) were produced and finished. Surface roughness Ra was determined via contact profilometry. Surface morphology was examined under a scanning electron microscope. Multi-species bacterial biofilms were grown on entire splints. Total biofilm mass and viable bacterial counts (CFU/ml) within the biofilms were determined. Statistical analyses were performed with a one-way ANOVA, Tukey's post hoc test, and Pearson's test (p < 0.05).

RESULTS

Astron CLEARsplint and KeySplint Soft specimens showed the highest surface roughness. The mean total biofilm mass on KeySplint Soft splints was higher compared to all other materials (p < 0.05). Colony-forming unit per milliliter on FuturaGen, Astron CLEARsplint, and KeySplint Soft splints was one log scale higher compared to all other materials. The other four printable resins displayed overall lower Ra, biofilm mass, and CFU/ml. A positive correlation was found between Ra and CFU/ml (r = 0.69, p = 0.04).

CONCLUSIONS

The 3D-printed splints showed overall favorable results regarding surface roughness and bacterial adhesion. Thermoplastic materials seem to display a higher surface roughness, making them more susceptible to microbial adhesion.

CLINICAL RELEVANCE

The development of caries and gingivitis in patients with oral appliances may be affected by the type of material.

Biofilm thickness controls the relative importance of stochastic and deterministic processes in microbial community assembly in moving bed biofilm reactors

Deterministic and stochastic processes are believed to play a combined role in microbial community assembly, though little is known about the factors determining their relative importance. We investigated the effect of biofilm thickness on community assembly in nitrifying moving bed biofilm reactors using biofilm carriers where maximum biofilm thickness is controlled. We examined the contribution of stochastic and deterministic processes to biofilm assembly in a steady state system using neutral community modelling and community diversity analysis with a null-modelling approach. Our results indicate that the formation of biofilms results in habitat filtration, causing selection for phylogenetically closely related community members, resulting in a substantial enrichment of Nitrospira spp. in the biofilm communities. Stochastic assembly processes were more prevalent in biofilms of 200 µm and thicker, while stronger selection in thinner (50 µm) biofilms could be driven by hydrodynamic and shear forces at the biofilm surface. Thicker biofilms exhibited greater phylogenetic beta-diversity, which may be driven by a variable selection regime caused by variation in environmental conditions between replicate carrier communities, or by drift combined with low migration rates resulting in stochastic historical contingency during community establishment. Our results indicate that assembly processes vary with biofilm thickness, contributing to our understanding of biofilm ecology and potentially paving the way towards strategies for microbial community management in biofilm systems.

Design strategy and mechanism of nitrite oxidation suppression of elevated loading rate partial nitritation system

There is a current need for a low operational intensity, effective and small footprint system to achieve stable partial nitritation for subsequent anammox treatment at mainstream municipal wastewaters. This research identifies a unique design strategy using an elevated total ammonia nitrogen (TAN) surface area loading rate (SALR) of 5 g TAN/m2.d to achieve cost-effective, stable, and elevated rates of partial nitritation in a moving bed biofilm reactor (MBBR) system under mainstream conditions. The elevated loaded partial nitritation MBBR system achieves a TAN surface area removal rate (SARR) of 2.01 ± 0.07 g TAN/m2.d and NO2−-N: NH4+-N stoichiometric ratio of 1.15:1, which is appropriate for downstream anammox treatment. The elevated TAN SALR design strategy promotes nitrite-oxidizing bacteria (NOB) activity suppression rather than a reduction in NOB population as the reason for the suppression of nitrite oxidation in the mainstream elevated loaded partial nitritation MBBR system. NOB activity is limited at an elevated TAN SALR likely due to thick biofilm embedding the NOB population and competition for dissolved oxygen (DO) with ammonia-oxidizing bacteria for TAN oxidation to nitrite within the biofilm structure, which ultimately limits the uptake of DO by NOB in the system. Therefore, this design strategy offers a cost-effective and efficient alternative for mainstream partial nitritation MBBR systems at water resource recovery facilities.

Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems

BACKGROUND

Microbial communities in recirculating aquaculture systems (RAS) play a role in system success, nutrient cycling, and water quality. Considering the increasing socio-economic role of fish farming, e.g., regarding food security, an in-depth understanding of aquaculture microbial communities is also relevant from a management perspective, especially regarding the growth, development, and welfare of the farmed animal. However, the current data on the composition of microbial communities within RAS is patchy, which is partly attributable to diverging method choices that render comparative analyses challenging. Therefore, there is a need for accurate, standardized, and user-friendly methods to study microbial communities in aquaculture systems.

RESULTS

We compared sequencing approach performances (3 types of 16S short amplicon sequencing, PacBio long-read amplicon sequencing, and amplification-free shotgun metagenomics) in the characterization of microbial communities in two commercial RAS fish farms. Results showed that 16S primer choice and amplicon length affect some values (e.g., diversity measures, number of assigned taxa or distinguishing ASVs) but have no impact on spatio-temporal patterns between sample types, farms and time points. This implies that 16S rRNA approaches are adequate for community studies. The long-read amplicons underperformed regarding the quantitative resolution of spatio-temporal patterns but were suited to identify functional services, e.g., nitrification cycling and the detection of pathogens. Finally, shotgun metagenomics extended the picture to fungi, viruses, and bacteriophages, opening avenues for exploring inter-domain interactions. All sequencing datasets agreed on major prokaryotic players, such as Actinobacteriota, Bacteroidota, Nitrospirota, and Proteobacteria.

CONCLUSION

The different sequencing approaches yielded overlapping and highly complementary results, with each contributing unique data not obtainable with the other approaches. We conclude that a tiered approach constitutes a strategy for obtaining the maximum amount of information on aquaculture microbial communities and can inform basic research on community evolution dynamics. For specific and/or applied questions, single-method approaches are more practical and cost-effective and could lead to better farm management practices.

Fabrication and characterization of a 3D polymicrobial microcosm biofilm model using melt electrowritten scaffolds

The majority of current biofilm models or substrates are two-dimensional (2D) and support biofilm growth in the horizontal plane only. Three-dimensional (3D) substrates may support both horizontal and vertical biofilm growth. This study compared biofilm growth quantity and quality between highly porous 3D micrometric fibrous scaffolds and 2D film substrates fabricated from medical grade polycaprolactone (mPCL). Melt electrowriting (MEW), a high-resolution additive manufacturing technology, was employed to design orderly aligned fine (~12 μm) fibre-based 3D scaffolds, while 2D films were fabricated by a casting method. The 3D scaffolds with a controlled pore size of 100 and 250 μm and thickness of ~0.8 mm and 2D films were incubated in pooled saliva collected from six volunteers for 1, 2, 4, 7 and 10 days at 37 °C to facilitate polymicrobial biofilm formation. Crystal violet assay demonstrated greater biofilm biomass in 3D MEW scaffolds than in 2D films. Biofilm thickness in 3D scaffolds was significantly higher compared to the biofilm thickness in 2D films. Both biovolume and substratum coverage of the biofilms was higher in the 3D scaffolds compared to 2D films. Polymeric bridges, pores, and channels characteristic of biofilms could be demonstrated by scanning electron microscopy. 16S rRNA sequencing demonstrated that the polymicrobial biofilms in the 3D scaffolds were able to retain 60-70 % of the original inoculum microbiome after 4 days. The MEW-fabricated 3D fibrous scaffold is a promising substrate for supporting multidirectional biofilm growth and modelling of a polymicrobial microcosm.

Microalgal extract as bio-coating to enhance biofilm growth of marine microalgae on microporous membranes

Microalgal biofilm is a popular platform for algal production, nutrient removal and carbon capture; however, it suffers from significant biofilm exfoliation under shear force exposure. Hence, a biologically-safe coating made up of algal extracellular polymeric substances (EPS) was utilized to secure the biofilm cell retention and cell loading on commercial microporous membrane (polyvinylidene fluoride), making the surfaces more hydrophobic (contact angle increase up to 12°). Results demonstrated that initial cell adhesion of three marine microalgae (Amphora coffeaeformis, Cylindrotheca fusiformis and Navicula incerta) was enhanced by at least 1.3 times higher than that of pristine control within only seven days with minimized biofilm exfoliation issue due to uniform distribution of sticky transparent exopolymer particles. Bounded extracellular polysaccharide gathered was approximately 23% higher on EPS-coated membranes to improve the biofilm's hydraulic resistance, whereas bounded extracellular protein would only be substantially elevated after the attached cells re-accommodate themselves onto the EPS pre-coating of themselves. In accounting the rises of hydrophobic protein content, biofilm was believed to be more stabilized, presumably via hydrophobic interactions. EPS biocoating would generate a groundswell of interest for bioprocess intensifications though there are lots of inherent technical and molecular challenges to be further investigated in future.

Environmental and ecological controls of the spatial distribution of microbial populations in aggregates

In microbial communities, the ecological interactions between species of different populations are responsible for the spatial distributions observed in aggregates (granules, biofilms or flocs). To explore the underlying mechanisms that control these processes, we have developed a mathematical modelling framework able to describe, label and quantify defined spatial structures that arise from microbial and environmental interactions in communities. An artificial system of three populations collaborating or competing in an aggregate is simulated using individual-based modelling under different environmental conditions. In this study, neutralism, competition, commensalism and concurrence of commensalism and competition have been considered. We were able to identify interspecific segregation of communities that appears in competitive environments (columned stratification), and a layered distribution of populations that emerges in commensal (layered stratification). When different ecological interactions were considered in the same aggregate, the resultant spatial distribution was identified as the one controlled by the most limiting substrate. A theoretical modulus was defined, with which we were able to quantify the effect of environmental conditions and ecological interactions to predict the most probable spatial distribution. The specific microbial patterns observed in our results allowed us to identify the optimal spatial organizations for bacteria to thrive when building a microbial community and how this permitted co-existence of populations at different growth rates. Our model reveals that although ecological relationships between different species dictate the distribution of bacteria, the environment controls the final spatial distribution of the community.

Characterizing and comparing microbial community and biofilm structure in three nitrifying moving bed biofilm reactors

This study investigated biofilm establishment, biofilm structure, and microbial community composition of biofilms in three laboratory-scale moving bed biofilm reactors. These reactors were filled with three types of plastic carriers with varied depths of living space for microbial growth. The reactors were operated under the same influent and operational conditions. Along with the operation, the results showed that carriers with grids of 50 μm in height delayed the biofilm development and formed the thinnest biofilm and a carpet-like structure with the lowest α-diversity. In comparison, another two carriers with grids of 200 and 400 μm in height formed thick biofilms and large colonies with more voids and channels. Quantified properties of biofilm thickness, biomass, heterogeneity, portion of the biofilm exposed to the nutrient, and maximum diffusion distance were examined, and the results demonstrated that they almost (except for heterogeneity) strongly correlated to the α-diversity of microbial community. These illustrate that depth of living space, as an important parameter for carrier, could drive the formation of biofilm structure and community composition. It improves understanding of influencing factors on biofilm establishment, structure and its microbial community, and would be helpful for the design of biofilm processes.

Simultaneous nitrification-denitrification in biofilm systems for wastewater treatment: Key factors, potential routes, and engineered applications

Simultaneous nitrification-denitrification (SND) is an advantageous bioprocess that allows the complete removal of ammonia nitrogen through sequential redox reactions leading to nitrogen gas production. SND can govern nitrogen removal in single-stage biofilm systems, such as the moving bed biofilm reactor and aerobic granular sludge system, as oxygen gradients allow the development of multilayered biofilms including nitrifying and denitrifying bacteria. Environmental and operational conditions can strongly influence SND performance, biofilm development and biochemical pathways. Recent advances have outlined the possibility to reduce the carbon and energy consumption of the process via the "shortcut pathway", and simultaneously remove both N and phosphorus under specific operational conditions, opening new possibilities for wastewater treatment. This work critically reviews the factors influencing SND and its application in biofilm systems from laboratory to full scale. Operational strategies to enhance SND efficiency and hints to reduce nitrous oxide emission and operational costs are provided.

Research trends and hotspots of aquatic biofilms in freshwater environment during the last three decades: a critical review and bibliometric analysis

Freshwater periphytic biofilms (FPBs), existing widely in various aquatic environments, have attracted extensive attention for many years. In the present study, a bibliometric analysis based on Web of Science Core Collection (WoSCC) was used to understand the research progress, trends, and hot topics of FPBs qualitatively and quantitatively. The results indicated that publications on FPBs have increased from 1991 to 2020 rapidly, and researchers have focused more on the areas of environmental sciences, microbiology, and marine freshwater biology. The most influential countries were mainly the USA, Spain, France, and Germany. Cooperation network analysis reflected that the USA and its affiliated institutions played crucial roles in the research of FPB cooperation, but the collaboration between core author groups still fell short. Based on the analysis of top 20 high-cited FPB documents over the last 30 years, research hotspots mainly included micro-observation and assembly mechanisms of FPBs; interactions of FPBs and pollutants including heavy metals, antibiotic resistance genes, pathogens, organic pollutants, and nanoparticles; and the role of FPBs for biogeochemical cycling, especially nitrogen cycling. Additionally, future research directions were proposed. Overall, this study provides a comprehensive and systematic overview of FPBs, which is useful for research development and researchers who are interested in this area.

Strategies to Improve the Potency of Oxazolidinones towards Bacterial Biofilms

Biofilms are part of the natural lifecycle of bacteria and are known to cause chronic infections that are difficult to treat. Most antibiotics are developed and tested against bacteria in the planktonic state and are ineffective against bacterial biofilms. The oxazolidinones, including the last resort drug linezolid, are one of the main classes of synthetic antibiotics progressed to clinical use in the last 50 years. They have a unique mechanism of action and only develop low levels of resistance in the clinical setting. With the aim of providing insight into strategies to design more potent antibiotic compounds with activity against bacterial biofilms, we review the biofilm activity of clinically approved oxazolidinones and report on structural modifications to oxazolidinones and their delivery systems which lead to enhanced anti-biofilm activity.

Metagenomic evidence of a novel family of anammox bacteria in a subsea environment

Bacteria in the order 'Candidatus Brocadiales' within the phylum Planctomycetes (Planctomycetota) have the remarkable ability to perform anaerobic ammonium oxidation (anammox). Two families of anammox bacteria with different biogeographical distributions have been reported, marine Ca. Scalinduaceae and freshwater Ca. Brocadiaceae. Here we report evidence of three new species within a novel genus and family of anammox bacteria, which were discovered in biofilms of a subsea road tunnel under a fjord in Norway. In this particular ecosystem, the nitrogen cycle is likely fuelled by ammonia from organic matter degradation in the fjord sediments and the rock mass above the tunnel, resulting in the growth of biofilms where anammox bacteria can thrive under oxygen limitation. We resolved several metagenome-assembled genomes (MAGs) of anammox bacteria, including three Ca. Brocadiales MAGs that could not be classified at the family level. MAGs of this novel family had all the diagnostic genes for a full anaerobic ammonium oxidation pathway in which nitrite was probably reduced by a NirK-like reductase. A survey of published molecular data indicated that this new family of anammox bacteria occurs in many marine sediments, where its members presumably would contribute to nitrogen loss.

Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems

Nitrification, the oxidation of ammonia to nitrate via nitrite, is important for many engineered water treatment systems. The sequential steps of this respiratory process are carried out by distinct microbial guilds, including ammonia-oxidizing bacteria (AOB) and archaea (AOA), nitrite-oxidizing bacteria (NOB), and newly discovered members of the genus Nitrospira that conduct complete ammonia oxidation (comammox). Even though all of these nitrifiers have been identified within water treatment systems, their relative contributions to nitrogen cycling are poorly understood. Although AOA contribute to nitrification in many wastewater treatment plants, they are generally outnumbered by AOB. In contrast, AOA and comammox Nitrospira typically dominate relatively low ammonia environments such as drinking water treatment, tertiary wastewater treatment systems, and aquaculture/aquarium filtration. Studies that focus on the abundance of ammonia oxidizers may misconstrue the actual role that distinct nitrifying guilds play in a system. Understanding which ammonia oxidizers are active is useful for further optimization of engineered systems that rely on nitrifiers for ammonia removal. This review highlights known distributions of AOA and comammox Nitrospira in engineered water treatment systems and suggests future research directions that will help assess their contributions to nitrification and identify factors that influence their distributions and activity.

Cannabigerol Effect on Streptococcus mutans Biofilms—A Computational Approach to Confocal Image Analysis

Biofilms are complex bacterial structures in which bacterial cells thrive as a community. Many bacterial species, including pathogens, form biofilms of high complexity and adaptability to a wide range of environmental conditions. One example of these is Streptococcus mutans, a gram-positive bacterium that has been associated with caries. Cannabigerol, a non-psychoactive cannabinoid, has been shown to affect S. mutans biofilms. In order to better characterize the effect of cannabigerol on biofilms of S. mutans, this paper provides a series of computational assays for biofilm analysis, applied on confocal images of S. mutans biofilms treated with cannabigerol. Confocal images are ubiquitous in biofilm analysis—they are often used to visualize the complex structure and molecular composition of biofilm macrocolonies. In this article, we demonstrate how confocal imaging data can be used to reveal more comprehensive insights into biofilm structure and measure specific anti-biofilm effects. This is accomplished by a series of computational assays, each focusing on a different aspect of biofilm structure.

Inactivation of E. coli, S. aureus, and Bacteriophages in Biofilms by Humidified Air Plasma

In this study, humidified air dielectric barrier discharge (DBD) plasma was used to inactivate Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), and bacteriophages in biofilms containing DNA, NaCl, carbohydrates, and proteins. The humidified DBD plasma was very effective in the inactivation of microbes in the (≤1.0 μm) biofilms. The number of surviving E. coli, S. aureus, and bacteriophages in the biofilms was strongly dependent on the constituent and thickness of the biofilms and was greatly reduced when the plasma treatment time increased from 5 s to 150 s. Our analysis shows that the UV irradiation was not responsible for the inactivation of microbes in biofilms. The short-lived RONS generated in the humidified air DBD plasma were not directly involved in the inactivation process; however, they recombined or reacted with other species to generate the long-lived RONS. Long-lived RONS diffused into the biofilms to generate very active species, such as ONOOH and OH. This study indicates that the geminated NO₂ and OH pair formed due to the homolysis of ONOOH can cause the synergistic oxidation of various organic molecules in the aqueous solution. Proteins in the biofilm were highly resistant to the inactivation of microbes in biofilms, which is presumably due to the existence of the unstable functional groups in the proteins. The unsaturated fatty acids, cysteine-rich proteins, and sulfur–methyl thioether groups in the proteins were easily oxidized by the geminated NO₂ and OH pair.

Modeling Virus and Bacteria Populations in Europa’s Subsurface Ocean

The search for life in the universe is often informed by the study of “extreme” environments on Earth, which provide analogs for habitable locations in the Solar System, and whose microbial inhabitants may therefore also serve as analogs for potential life forms in extraterrestrial milieus. Recent work has highlighted the ubiquity and importance of viral entities in terrestrial ecosystems, which calls for a greater understanding of the roles that viruses might play in hypothetical extraterrestrial biomes. While some studies have modeled the dynamics of viral and bacterial populations in icy ocean environments on Earth, previous work has yet to apply these findings to icy ocean worlds such as Jupiter’s moon Europa. It is commonly theorized that hydrothermal vents on Europa could produce the necessary reductants for chemosynthesis to take place on the ocean bottom. In the case that Europa’s ocean is a reductant-limited environment, how might reductants and organic matter reach the sub-ice region to power a more easily accessible ecosystem? Here, we propose a ‘viral elevator,’ a mechanism that functions similarly to the ‘viral shunt’ in Earth’s oceans, which could create and shuttle dissolved organic matter (DOM) to a hypothetical sub-ice biosphere through viral carriers. Current models of Europa’s ocean currents and stratification support the movement of DOM to the sub-ice biosphere. We adapt an existing model for bacterial and viral population dynamics in Earth’s Arctic sea ice to Europa and use parameters from various Arctic-based studies as proxies for Europa’s environment. We find that viral burst size has the most significant effect on the virus-to-bacteria ratio (VBR) and system longevity in closed systems (such as brine pockets within Europa’s icy crust), with higher burst sizes clearly increasing both. When applying our model to an open system with an influx of DOM from the viral elevator, we found that a steady-state system is attainable, with resulting sub-ice biofilms on the order of 0.1 mm thick (global equivalent layer). This has implications for future searches for life on Europa, given that life directly under the ice will be easier to detect and observe than life near the ocean bottom.

Biofilm phenotypes and internal community succession determines distinct growth of anammox bacteria in functional anammox biofilms

In this study, time-series anammox functional biofilms were obtained in a lab-scale simultaneous partial nitritation/anammox process for treating high-strength ammonium. The variations in the biofilm phenotypes, community succession, and anammox bacteria abundance over time were evaluated using optical microscopy, 16S rRNA gene sequencing, and qPCR. The result revealed that biofilm has three distinct stages of the community development trajectory across a 182-day temporal scale. Anammox bacteria growth rates were 0.035 d^-1, 0.0015 d^-1, and 0.011 d^-1, respectively. The diversity and network analysis suggested that the positive priority effect of ammonia oxidizing bacteria was the primary factor for the rapid proliferation of anammox bacteria, and the species replacement triggering priority effect forfeiture and substituted functional recruitment were reasons for the slow proliferation and stable proliferation of anammox bacteria, respectively. Taken together, the higher microbial diversity and stable community composite were key prerequisites for the proliferation of the anammox bacteria.

Solid-State NMR Investigations of Extracellular Matrixes and Cell Walls of Algae, Bacteria, Fungi, and Plants

Extracellular matrixes (ECMs), such as the cell walls and biofilms, are important for supporting cell integrity and function and regulating intercellular communication. These biomaterials are also of significant interest to the production of biofuels and the development of antimicrobial treatment. Solid-state nuclear magnetic resonance (ssNMR) and magic-angle spinning-dynamic nuclear polarization (MAS-DNP) are uniquely powerful for understanding the conformational structure, dynamical characteristics, and supramolecular assemblies of carbohydrates and other biomolecules in ECMs. This review highlights the recent high-resolution investigations of intact ECMs and native cells in many organisms spanning across plants, bacteria, fungi, and algae. We spotlight the structural principles identified in ECMs, discuss the current technical limitation and underexplored biochemical topics, and point out the promising opportunities enabled by the recent advances of the rapidly evolving ssNMR technology.

New Trends in Photodynamic Inactivation (PDI) Combating Biofilms in the Food Industry-A Review

Biofilms cause problems in the food industry due to their persistence and incompetent hygiene processing technologies. Interest in photodynamic inactivation (PDI) for combating biofilms has increased in recent years. This technique can induce microbial cell death, reduce cell attachment, ruin biofilm biomolecules and eradicate structured biofilms without inducing microbial resistance. This review addresses microbial challenges posed by biofilms in food environments and highlights the advantages of PDI in preventing and eradicating microbial biofilm communities. Current findings of the antibiofilm efficiencies of this technique are summarized. Additionally, emphasis is given to its potential mechanisms and factors capable of influencing biofilm communities, as well as promising hurdle strategies.

Using anammox biofilms for rapid start-up of partial nitritation-anammox in integrated fixed-film activated sludge for autotrophic nitrogen removal

Integrated fixed-film activated sludge (IFAS) reactors are suitable for partial nitritation-anammox (PNA) for autotrophic nitrogen removal; however, its start-up and biofilm formation are slow and difficult. In this study, a new sludge seeding strategy was developed for the start-up of PNA-IFAS by using the pre-cultivated anammox biofilms. Two bioreactors were used in the experimental study, including a reactor that was started conventionally with the pre-acclimated suspended PNA sludge and bare biocarriers (PA-S) and a reactor that used the new seeding method with anammox biofilms pre-acclimated on biocarriers and ammonia-oxidizing bacteria (AOB) sludge in the suspension (PA-B). The use of anammox biofilms as the seed biomass greatly shortened the start-up period of the PNA-IFAS reactor to 1 month or so. Moreover, reactor PA-B achieved a higher nitrogen removal rate (707.3 mg N/(L·d)), better nitrogen removal efficiency (86.8 ± 2.8%), and lower nitrate yield (9.4%) than reactor PA-S. The biofilm development in PA-B was accelerated and its biofilm content was nearly 10 times higher than that of PA-S. The initial segregation of anammox in the biofilm and AOB in the suspended sludge provided an environment that not only accelerated the start-up of PNA-IFAS but also helped suppress the enrichment of unwanted nitrite-oxidizing bacteria (NOB) in the bioreactor, as evidenced by the lower NOB abundance in PA-B (<0.5%) than in PA-S (>2.2%) according to microbial community analysis.

Relative Importance of Stochastic Assembly Process of Membrane Biofilm Increased as Biofilm Aged

The relative importance of different ecological processes controlling biofilm community assembly over time on membranes with different surface characteristics has never been investigated in membrane bioreactors (MBRs). In this study, five ultrafiltration hollow-fiber membranes - having identical nominal pore size (0.1μm) but different hydrophobic or hydrophilic surface characteristics - were operated simultaneously in the same MBR tank with a constant flux of 10 liters per square meter per hour (LMH). In parallel, membrane modules operated without permeate flux (0 LMH) were submerged in the same MBR tank, to investigate the passive microbial adsorption onto different hydrophobic or hydrophilic membranes. Samples from the membrane biofilm were collected after 1, 10, 20, and 30days of continuous filtration. The membrane biofilm microbiome were investigated using 16S rRNA gene amplicon sequencing from DNA and cDNA samples. Similar beta diversity trends were observed for both DNA- and cDNA-based analyses. Beta diversity analyses revealed that the nature of the membrane surface (i.e., hydrophobic vs. hydrophilic) did not seem to have an effect in shaping the bacterial community, and a similar biofilm microbiome evolved for all types of membranes. Similarly, membrane modules operated with and without permeate flux did not significantly influence alpha and beta diversity of the membrane biofilm. Nevertheless, different-aged membrane biofilm samples exhibited significant differences. Proteobacteria was the most dominant phylum in early-stage membrane biofilm after 1 and 10days of filtration. Subsequently, the relative reads abundance of the phyla Bacteroidetes and Firmicutes increased within the membrane biofilm communities after 20 and 30days of filtration, possibly due to successional steps that lead to the formation of a relatively aged biofilm. Our findings indicate distinct membrane biofilm assembly patterns with different-aged biofilm. Ecological null model analyses revealed that the assembly of early-stage biofilm community developed after 1 and 10days of filtration was mainly governed by homogenous selection. As the biofilm aged (days 20 and 30), stochastic processes (e.g., ecological drift) started to become important in shaping the assembly of biofilm community.

Relevance of Candidatus Nitrotoga for nitrite oxidation in technical nitrogen removal systems

Abstract

Many biotechnological applications deal with nitrification, one of the main steps of the global nitrogen cycle. The biological oxidation of ammonia to nitrite and further to nitrate is critical to avoid environmental damage and its functioning has to be retained even under adverse conditions. Bacteria performing the second reaction, oxidation of nitrite to nitrate, are fastidious microorganisms that are highly sensitive against disturbances. One important finding with relevance for nitrogen removal systems was the discovery of the mainly cold-adapted Cand. Nitrotoga, whose activity seems to be essential for the recovery of nitrite oxidation in wastewater treatment plants at low temperatures, e.g., during cold seasons. Several new strains of this genus have been recently described and ecophysiologically characterized including genome analyses. With increasing diversity, also mesophilic Cand. Nitrotoga representatives have been detected in activated sludge. This review summarizes the natural distribution and driving forces defining niche separation in artificial nitrification systems. Further critical aspects for the competition with Nitrospira and Nitrobacter are discussed. Knowledge about the physiological capacities and limits of Cand. Nitrotoga can help to define physico-chemical parameters for example in reactor systems that need to be run at low temperatures.

Key points

• Characterization of the psychrotolerant nitrite oxidizer Cand. Nitrotoga

• Comparison of the physiological features of Cand. Nitrotoga with those of other NOB

• Identification of beneficial environmental/operational parameters for proliferation

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11487-5.

Recent advancements in the biological treatment of high strength ammonia wastewater

The estimated global population growth of 81 million people per year, combined with increased rates of urbanization and associated industrial processes, result in volumes of high strength ammonia wastewater that cannot be treated in a cost-effective or sustainable manner using the floc-based conventional activated sludge approach of nitrification and denitrification. Biofilm and aerobic granular sludge technologies have shown promise to significantly improve the performance of biological nitrogen removal systems treating high strength wastewater. This is partly due to enhanced biomass retention and their ability to sustain diverse microbial populations with juxtaposing growth requirements. Recent research has also demonstrated the value of hybrid systems with heterogeneous bioaggregates to mitigate biofilm and granule instability during long-term operation. In the context of high strength ammonia wastewater treatment, conventional nitrification-denitrification is hampered by high energy costs and greenhouse gas emissions. Anammox-based processes such as partial nitritation-anammox and partial denitrification-anammox represent more cost-effective and sustainable methods of removing reactive nitrogen from wastewater. There is also growing interest in the use of photosynthetic bacteria for ammonia recovery from high strength waste streams, such that nitrogen can be captured and concentrated in its reactive form and recycled into high value products. The purpose of this review is to explore recent advancements and emerging approaches related to high strength ammonia wastewater treatment.

Promoting the degradation of organic micropollutants in tertiary moving bed biofilm reactors by controlling growth and redox conditions

A novel process configuration was designed to increase biofilm growth in tertiary moving bed biofilm reactors (MBBRs) by providing additional substrate from primary treated wastewater in a sidestream reactor under different redox conditions in order to improve micropollutant removal in MBBRs with low substrate availability. This novel recirculating MBBR was operated on pilot scale for 13 months, and a systematic increase was seen in the biomass concentration and the micropollutant degradation rates, compared to a tertiary MBBR without additional substrate. The degradation rates per unit carrier surface area increased in the order of ten times, and for certain micropollutants, such as atenolol, metoprolol, trimethoprim and roxithromycin, the degradation rates increased 20-60 times. Aerobic conditions were critical for maintaining high micropollutant degradation rates. With innovative MBBR configurations it may be possible to improve the biological degradation of organic micropollutants in wastewater. It is suggested that degradation rates be normalized to the carrier surface area, in favor of the biomass concentration, as this reflects the diffusion limitations of oxygen, and will facilitate the comparison of different biofilm systems.

Microbial biofilms in biorefinery - Towards a sustainable production of low-value bulk chemicals and fuels

Harnessing the potential of biocatalytic conversion of renewable biomass into value-added products is still hampered by unfavorable process economics. This has promoted the use of biofilms as an alternative to overcome the limitations of traditional planktonic systems. In this paper, the benefits and challenges of biofilm fermentations are reviewed with a focus on the production of low-value bulk chemicals and fuels from waste biomass. Our study demonstrates that biofilm fermentations can potentially improve productivities and product yields by increasing biomass retention and allowing for continuous operation at high dilution rates. Furthermore, we show that biofilms can tolerate hazardous environments, which improve the conversion of crude biomass under substrate and product inhibitory conditions. Additionally, we present examples for the improved conversion of pure and crude substrates into bulk chemicals by mixed microbial biofilms, which can benefit from microenvironments in biofilms for synergistic multi-species reactions, and improved resistance to contaminants. Finally, we suggest the use of mathematical models as useful tools to supplement experimental insights related to the effects of physico-chemical and biological phenomena on the process. Major challenges for biofilm fermentations arise from inconsistent fermentation performance, slow reactor start-up, biofilm carrier costs and carrier clogging, insufficient biofilm monitoring and process control, challenges in reactor sterilization and scale-up, and issues in recovering dilute products. The key to a successful commercialization of the technology is likely going to be an interdisciplinary approach. Crucial research areas might include genetic engineering combined with the development of specialized biofilm reactors, biofilm carrier development, in-situ biofilm monitoring, model-based process control, mixed microbial biofilm technology, development of suitable biofilm reactor scale-up criteria, and in-situ product recovery.

Mimicking biofilm formation and development: Recent progress in in vitro and in vivo biofilm models

Biofilm formation in living organisms is associated to tissue and implant infections, and it has also been linked to the contribution of antibiotic resistance. Thus, understanding biofilm development and being able to mimic such processes is vital for the successful development of antibiofilm treatments and therapies. Several decades of research have contributed to building the foundation for developing in vitro and in vivo biofilm models. However, no such thing as an "all fit" in vitro or in vivo biofilm models is currently available. In this review, in addition to presenting an updated overview of biofilm formation, we critically revise recent approaches for the improvement of in vitro and in vivo biofilm models.

Unveiling the Antifouling Performance of Different Marine Surfaces and Their Effect on the Development and Structure of Cyanobacterial Biofilms

Since biofilm formation by microfoulers significantly contributes to the fouling process, it is important to evaluate the performance of marine surfaces to prevent biofilm formation, as well as understand their interactions with microfoulers and how these affect biofilm development and structure. In this study, the long-term performance of five surface materials—glass, perspex, polystyrene, epoxy-coated glass, and a silicone hydrogel coating—in inhibiting biofilm formation by cyanobacteria was evaluated. For this purpose, cyanobacterial biofilms were developed under controlled hydrodynamic conditions typically found in marine environments, and the biofilm cell number, wet weight, chlorophyll a content, and biofilm thickness and structure were assessed after 49 days. In order to obtain more insight into the effect of surface properties on biofilm formation, they were characterized concerning their hydrophobicity and roughness. Results demonstrated that silicone hydrogel surfaces were effective in inhibiting cyanobacterial biofilm formation. In fact, biofilms formed on these surfaces showed a lower number of biofilm cells, chlorophyll a content, biofilm thickness, and percentage and size of biofilm empty spaces compared to remaining surfaces. Additionally, our results demonstrated that the surface properties, together with the features of the fouling microorganisms, have a considerable impact on marine biofouling potential.

Supplemental nutrients stimulate the amplification of carbapenemase-producing Klebsiella pneumoniae (CPKP) in a sink drain in vitro biofilm reactor model

Liquid wastes (LW) disposed in hospital handwashing sinks may affect colonization of sink P-traps by carbapenemase-producing Klebsiella pneumoniae (CPKP), causing CPKP dispersal into the patient care environment. This study aimed to determine the effect of LW on biofilm formation and CPKP colonization in a P-Trap model (PTM). PTMs containing polymicrobial biofilms grown in autoclaved municipal tap water (ATW) supplemented with 5% dextrose in water (D5W), nutritional shake (Shake), sugar-based soft drink (Soda), or ATW were inoculated with K. pneumoniae ST258 KPC+ (ST258) or K. pneumoniae CAV1016 (CAV1016) and sampled after 7, 14, and 21 d. Biofilm bio-volume, mean thickness, and heterotrophic plate counts were significantly reduced and roughness coefficient significantly increased by Soda compared with D5W, Shake, or ATW. CPKP were significantly reduced by Soda but significantly amplified by D5W (ST258; CAV1016, 7 d) and Shake (ST258) suggesting that reducing LW disposal in sinks may reduce CPKP dispersal into patient care environments.

Biodegradation of organophosphorus pesticides in moving bed biofilm reactors: Analysis of microbial community and biodegradation pathways

We investigated the performance of a lab-scale moving bed biofilm reactor (MBBR) with respect to general bioconversion processes and biotransformation of two commonly used organophosphorus pesticides, Chlorpyrifos (CHL) and Malathion (MAL). The reactor was operated for 300 days under different organic loads by changing hydraulic retention time (HRT). The decrease in organic load resulted in the formation of a thinner biofilm and the growth of more biomass in the bulk, which greatly shifted bioconversion processes. The low organic loading supported more nitrification in the reactor, but an opposite trend was observed for denitrification, which was enhanced at higher organic loading where the formation of anoxic zones in the thick biofilm was favored. 70% and 55% removal corresponding to 210 and 165 µg/m²/d occurred for MAL and CHL, respectively, at an HRT of 3 h and progressively increased with higher HRTs. Phylogenetic analysis revealed a shift in composition and abundance of taxa throughout the reactor operation where lower loading rate supported the growth of a more diverse and evenly distributed community. The analysis also highlighted the dominance of heterotrophic communities such as Flavobacterium and Acinetobacter johnsonii, which could be involved in the biotransformation of CHL and MAL through co-metabolism.

Microbial Diversity and Mercury Methylation Activity in Periphytic Biofilms at a Run-of-River Hydroelectric Dam and Constructed Wetlands

Periphytic biofilms have the potential to greatly influence the microbial production of the neurotoxicant monomethylmercury in freshwaters although few studies have simultaneously assessed periphyton mercury methylation and demethylation rates and the microbial communities associated with these transformations. We performed a field study on periphyton from a river affected by run-of-river power plants and artificial wetlands in a boreal landscape (Québec, Canada). In situ incubations were performed on three sites using environmental concentrations of isotopically enriched monomethylmercury (MM198Hg) and inorganic mercury (200Hg) for demethylation and methylation rate measurements. Periphytic microbial communities were investigated through 16S rRNA gene analyses and metagenomic screenings for the hgcA gene, involved in mercury methylation. Positive mercury methylation rates ([5.9 ± 3.4] × 10-3 day-1) were observed only in the wetlands, and demethylation rates averaged 1.78 ± 0.21 day-1 for the three studied sites. The 16S rRNA gene analyses revealed Proteobacteria as the most abundant phylum across all sites (36.3% ± 1.4%), from which families associated with mercury methylation were mostly found in the wetland site. Metagenome screening for HgcA identified 24 different hgcA sequences in the constructed wetland site only, associated with 8 known families, where the iron-reducing Geobacteraceae were the most abundant. This work brings new information on mercury methylation in periphyton from habitats of impacted rivers, associating it mostly with putative iron-reducing bacteria.IMPORTANCE Monomethylmercury (MMHg) is a biomagnifiable neurotoxin of global concern with risks to human health mostly associated with fish consumption. Hydroelectric reservoirs are known to be sources of MMHg many years after their impoundment. Little is known, however, on run-of-river dams flooding smaller terrestrial areas, although their numbers are expected to increase considerably worldwide in decades to come. Production of MMHg is associated mostly with anaerobic processes, but Hg methylation has been shown to occur in periphytic biofilms located in oxic zones of the water column. Therefore, in this study, we investigated in situ production of MMHg by periphytic communities in habitats impacted by the construction of a run-of-river dam by combining transformation rate measurements with genomic approaches targeting hgcAB genes, responsible for mercury methylation. These results provide extended knowledge on mercury methylators in river ecosystems impacted by run-of-river dams in temperate habitats.

Interactions of plasma-activated water with biofilms: inactivation, dispersal effects and mechanisms of action

Biofilms have several characteristics that ensure their survival in a range of adverse environmental conditions, including high cell numbers, close cell proximity to allow easy genetic exchange (e.g., for resistance genes), cell communication and protection through the production of an exopolysaccharide matrix. Together, these characteristics make it difficult to kill undesirable biofilms, despite the many studies aimed at improving the removal of biofilms. An elimination method that is safe, easy to deliver in physically complex environments and not prone to microbial resistance is highly desired. Cold atmospheric plasma, a lightning-like state generated from air or other gases with a high voltage can be used to make plasma-activated water (PAW) that contains many active species and radicals that have antimicrobial activity. Recent studies have shown the potential for PAW to be used for biofilm elimination without causing the bacteria to develop significant resistance. However, the precise mode of action is still the subject of debate. This review discusses the formation of PAW generated species and their impacts on biofilms. A focus is placed on the diffusion of reactive species into biofilms, the formation of gradients and the resulting interaction with the biofilm matrix and specific biofilm components. Such an understanding will provide significant benefits for tackling the ubiquitous problem of biofilm contamination in food, water and medical areas.

Experimental and computational approaches to unravel microbial community assembly

Microbial communities have a preponderant role in the life support processes of our common home planet Earth. These extremely diverse communities drive global biogeochemical cycles, and develop intimate relationships with most multicellular organisms, with a significant impact on their fitness. Our understanding of their composition and function has enjoyed a significant thrust during the last decade thanks to the rise of high-throughput sequencing technologies. Intriguingly, the diversity patterns observed in nature point to the possible existence of fundamental community assembly rules. Unfortunately, these rules are still poorly understood, despite the fact that their knowledge could spur a scientific, technological, and economic revolution, impacting, for instance, agricultural, environmental, and health-related practices. In this minireview, I recapitulate the most important wet lab techniques and computational approaches currently employed in the study of microbial community assembly, and briefly discuss various experimental designs. Most of these approaches and considerations are also relevant to the study of microbial microevolution, as it has been shown that it can occur in ecological relevant timescales. Moreover, I provide a succinct review of various recent studies, chosen based on the diversity of ecological concepts addressed, experimental designs, and choice of wet lab and computational techniques. This piece aims to serve as a primer to those new to the field, as well as a source of new ideas to the more experienced researchers.

Integrating Microbial Community Assembly and Fluid Kinetics to Decouple Nitrogen Dynamics in an Urban Channel Confluence

Understanding the characteristics of biogeochemical processes in urban channel confluences is essential for the evaluation and improvement of water environmental capacity. However, influences of biogeochemical processes in confluence were always overlooked or simply parametrized since the transformation processes controlled by microbial community assembly were hard to quantify. To address this knowledge gap, the present study proposed a novel mathematical modeling system, based on microbial community assembly theory and fluid kinetics, to decouple nitrogen dynamics into flow-induced transport and microorganism-induced transformation processes, and quantified their contributions to nitrogen concentrations. Results revealed that variable selection processes (including hydrodynamic conditions) contributed to significant difference in microbial communities among different hydraulic regions. Variation in microbial communities further shifted transformation processes. Rhodobacterales and Sphingomonadales, which were reported to be vital participants in denitrification process, were enriched in flow separation region, and promoted it as a hotspot for nitrogen removal. In the flow separation region, microorganism-induced transformation processes accounted for 56% of total nitrogen removal, which was significantly higher than that in other regions (12% on average; p < 0.01). Results and findings could provide useful information for the improvement of water environmental capacity.

Technologies for biological removal and recovery of nitrogen from wastewater

Water contamination is a growing environmental issue. Several harmful effects on human health and the environment are attributed to nitrogen contamination of water sources. Consequently, many countries have strict regulations on nitrogen compound concentrations in wastewater effluents. Wastewater treatment is carried out using energy- and cost-intensive biological processes, which convert nitrogen compounds into innocuous dinitrogen gas. On the other hand, nitrogen is also an essential nutrient. Artificial fertilizers are produced by fixing dinitrogen gas from the atmosphere, in an energy-intensive chemical process. Ideally, we should be able to spend less energy and chemicals to remove nitrogen from wastewater and instead recover a fraction of it for use in fertilizers and similar applications. In this review, we present an overview of various technologies of biological nitrogen removal including nitrification, denitrification, anaerobic ammonium oxidation (anammox), as well as bioelectrochemical systems and microalgal growth for nitrogen recovery. We highlighted the nitrogen removal efficiency of these systems at different temperatures and operating conditions. The advantages, practical challenges, and potential for nitrogen recovery of different treatment methods are discussed.

Analysis of three-dimensional biofilms on different material surfaces

Biofilms cause complications and high costs in both industry and medicine. Of particular interest are bacterial infections of prosthetic materials, which usually cannot be eliminated due to the high antibiotic resistance known for bacteria forming biofilms. The search for new materials and coatings with lower colonization potential and antibacterial activity is of great importance to reduce biofilm formation. However, there is no standardized procedure to examine the colonization characteristics of bacteria in the biofilm state in situ. Here, we describe an automated epifluorescence microscopy system for the semi-quantitative analysis of three-dimensional (3D) biofilms on various surfaces. To analyze adherent bacteria, three materials (glass, steel and titanium) were incubated with bacteria in a flow chamber system. After fluorescence staining of the bacteria, automated image capturing, quantification of the bacteria, measurement of the colonized area and determination of the 3D biofilm height were carried out by using novel software. Furthermore, the materials were examined for their surface topography using white light scanning interferometry. Titanium compared to glass showed a significantly higher number of adherent bacteria. We argue that this was due to the higher microroughness of titanium. The colonized area was in accordance with the number of adherent bacteria and was also significantly larger on titanium coupons compared to glass. Maximum 3D biofilm height on glass coupons was significantly lower compared to the ones on steel and titanium. This novel method enables the standardized, automated investigation of the colonization with bacteria on different materials. This approach can considerably support the characterization of new material surfaces and their innovative coatings by analyzing the amount of attached bacteria and thickness of biofilms in situ and eliminates the need of conventional cultivation.

Ecological Processes Affecting Long-Term Eukaryote and Prokaryote Biofilm Persistence in Nitrogen Removal from Sewage

The factors affecting long-term biofilm stability in sewage treatment remain largely unexplored. We therefore analyzed moving bed bioreactors (MBBRs) biofilm composition and function two years apart from four reactors in a nitrogen-removal sewage treatment plant. Multivariate ANOVA revealed a similar prokaryote microbiota composition on biofilm carriers from the same reactors, where reactor explained 84.6% of the variance, and year only explained 1.5%. Eukaryotes showed a less similar composition with reactor explaining 56.8% of the variance and year 9.4%. Downstream effects were also more pronounced for eukaryotes than prokaryotes. For prokaryotes, carbon source emerged as a potential factor for deterministic assembly. In the two reactors with methanol as a carbon source, the bacterial genus Methylotenera dominated, with M. versatilis as the most abundant species. M. versatilis showed large lineage diversity. The lineages mainly differed with respect to potential terminal electron acceptor usage (nitrogen oxides and oxygen). Searches in the Sequence Read Archive (SRA) database indicate a global distribution of the M. versatilis strains, with methane-containing sediments as the main habitat. Taken together, our results support long-term prokaryote biofilm persistence, while eukaryotes were less persistent.

Photodynamic Activity on Biofilm in Endotracheal Tubes of Patients Admitted to an Intensive Care Unit

Ventilator-associated pneumonia (VAP) is an infection that arises after endotracheal intubation affecting patients under intensive care. The presence of the endotracheal tube (ETT) is a risk factor since it is colonized by multispecies biofilm. Antimicrobial photodynamic therapy (aPDT) could be a strategy to decontaminate ETTs. We verify if methylene blue (MB) associated with external illumination of the ETT could be an alternative to destroy biofilm. We performed an in vitro and ex vivo study. In vitro study was performed with P. aeruginosa biofilm grew over ETT for 7 days. After treatment, the surviving cells were cultured for 3 days and the biofilm was analyzed by crystal violet absorbance. Ex vivo study employed ETT obtained from extubated patients. aPDT was performed with MB (100 µm) and red LED (λ = 640±20 nm). We quantified the biofilm thickness and used scanning electron microscopy and fluorescence technique to verify morphological and functional changes after aPDT. Our results showed that bacteria remain susceptible to aPDT after sequential treatments. We also attested that aPDT can reduce biofilm thickness, disrupt biofilm attachment from ETT surface and kill microbial cells. These data suggest that aPDT should be investigated to decrease VAP incidence via ETT decontamination.

Poised potential is not an effective strategy to enhance bio-electrochemical denitrification under cyclic substrate limitations

Bio-electrochemical denitrification (BED) is a promising organic carbon-free nitrate remediation technology. However, the relationship between engineering conditions, biofilm community composition, and resultant functions in BED remains under-explored. This study used deep sequencing and variation partitioning analysis to investigate the compositional shifts in biofilm communities under varied poised potentials in the batch mode, and correlated these shifts to reactor-level functional differences. Interestingly, the results suggest that the proliferation of a key species, Thiobacillus denitrificans, and community diversity (the Shannon index), were almost equally important in explaining the reactor-to-reactor functional variability (e.g. variability in denitrification rates was 51% and 38% attributable to key species and community diversity respectively, with a 30% overlap), but neither was heavily impacted by the poised potential. The findings suggest that while enriching the key species may be critical in improving the functional efficiency of BED, poised potentials may not be an effective strategy to achieve the desired level of enrichment in substrate-limited real-world conditions.