Biofilm Communities Research Articles

Stronger biogeographical pattern of bacterioplankton communities than biofilm communities along a riverine ecosystem: a local scale study of the Kaidu river in the arid and semi-arid northwest of China

Although the biogeographical pattern and mechanisms underlying microbial assembly have been well-explored in lentic ecosystems, the relevant scenarios in lotic ecosystems remain poorly understood. By sequencing the bacterial communities in bacterioplankton and biofilm, our study detected their distance-decay relationship (DDR), and the balance between deterministic and stochastic processes, along the Kaidu river in an arid and semi-arid region of northwest China. Our results revealed that bacterioplankton and biofilm had significantly contrasting community structures. The bacterioplankton communities showed a gradually decreasing trend in alpha-diversity from the headwater to the river mouth, contrasting with the alpha-diversity of biofilm communities which was constant along the river length. Both bacterioplankton and biofilm showed significant DDRs along the 500-km river corridor with the slope of the bacterioplankton DDR being steeper than that of the biofilm DDR, which implies a stronger biogeography of bacterioplankton than biofilm. Relative to biofilm communities, the species interactions formed a denser and more complex network in the bacterioplankton communities than in the biofilm communities. Our results also revealed that there was a transition of community assembly from deterministic to stochastic processes upstream to downstream, although both the bacterioplankton and biofilm communities were mainly regulated by deterministic processes within the entire river. All these empirical results expand our knowledge of microbial ecology in an arid and semi-arid lotic ecosystem.

Optogenetic patterning generates multi-strain biofilms with spatially distributed antibiotic resistance

Spatial organization of microbes in biofilms enables crucial community function such as division of labor. However, quantitative understanding of such emergent community properties remains limited due to a scarcity of tools for patterning heterogeneous biofilms. Here we develop a synthetic optogenetic toolkit ‘Multipattern Biofilm Lithography’ for rational engineering and orthogonal patterning of multi-strain biofilms, inspired by successive adhesion and phenotypic differentiation in natural biofilms. We apply this toolkit to profile the growth dynamics of heterogeneous biofilm communities, and observe the emergence of spatially modulated commensal relationships due to shared antibiotic protection against the beta-lactam ampicillin. Supported by biophysical modeling, these results yield in-vivo measurements of key parameters, e.g., molecular beta-lactamase production per cell and length scale of antibiotic zone of protection. Our toolbox and associated findings provide quantitative insights into the spatial organization and distributed antibiotic protection within biofilms, with direct implications for future biofilm research and engineering.

Metabolic interplay between Proteus mirabilis and Enterococcus faecalis facilitates polymicrobial biofilm formation and invasive disease.

Biofilms play an important role in the development and pathogenesis of catheter-associated urinary tract infection (CAUTI). Proteus mirabilis and Enterococcus faecalis are common CAUTI pathogens that persistently co-colonize the catheterized urinary tract and form biofilms with increased biomass and antibiotic resistance. In this study, we uncover the metabolic interplay that drives biofilm enhancement and examine the contribution to CAUTI severity. Through compositional and proteomic biofilm analyses, we determined that the increase in biofilm biomass stems from an increase in the protein fraction of the polymicrobial biofilm. We further observed an enrichment in proteins associated with ornithine and arginine metabolism in polymicrobial biofilms compared with single-species biofilms. We show that arginine/ornithine antiport by E. faecalis promotes arginine biosynthesis and metabolism in P. mirabilis, ultimately driving the increase in polymicrobial biofilm protein content without affecting viability of either species. We further show that disrupting E. faecalis ornithine antiport alters the metabolic profile of polymicrobial biofilms and prevents enhancement, and this defect was complemented by supplementation with exogenous ornithine. In a murine model of CAUTI, ornithine antiport did not contribute to E. faecalis colonization but was required for the increased incidence of urinary stone formation and bacteremia that occurs during polymicrobial CAUTI with P. mirabilis. Thus, disrupting metabolic interplay between common co-colonizing species may represent a viable strategy for reducing risk of bacteremia.IMPORTANCEChronic infections often involve the formation of antibiotic-resistant biofilm communities that include multiple different microbes, which pose a challenge for effective treatment. In the catheterized urinary tract, potential pathogens persistently co-colonize for long periods of time and the interactions between them can lead to more severe disease outcomes. In this study, we identified the metabolite L-ornithine as a key mediator of disease-enhancing interactions between two common and challenging pathogens, Enterococcus faecalis and Proteus mirabilis. Disrupting ornithine-mediated interactions may therefore represent a strategy to prevent polymicrobial biofilm formation and decrease risk of severe disease.

The bacterial strains JAM1T and GP59 of the species Methylophaga nitratireducenticrescens differ in their expression profiles of denitrification genes in oxic and anoxic cultures.

Strain JAM1T and strain GP59 of the methylotrophic, bacterial species Methylophaga nitratireducenticrescens were isolated from a microbial community of the biofilm that developed in a fluidized-bed, methanol-fed, marine denitrification system. Despite of their common origin, both strains showed distinct physiological characters towards the dynamics of nitrate ( ) reduction. Strain JAM1T can reduce to nitrite ( ) but not to nitric oxide (NO) as it lacks a NO-forming reductase. Strain GP59 on the other hand can carry the complete reduction of to N2. Strain GP59 cultured under anoxic conditions shows a 24-48h lag phase before reduction occurs. In strain JAM1T cultures, reduction begins immediately with accumulation of . Furthermore, is reduced under oxic conditions in strain JAM1T cultures, which does not appear in strain GP59 cultures. These distinct characters suggest differences in the regulation pathways impacting the expression of denitrification genes, and ultimately growth. Both strains were cultured under oxic conditions either with or without , or under anoxic conditions with . Transcript levels of selected denitrification genes (nar1 and nar2 encoding reductases, nirK encoding reductase, narK12f encoding / transporter) and regulatory genes (narXL and fnr) were determined by quantitative reverse transcription polymerase chain reaction. We also derived the transcriptomes of these cultures and determined their relative gene expression profiles. The transcript levels of nar1 were very low in strain GP59 cultured under oxic conditions without . These levels were 37 times higher in strain JAM1T cultured under the same conditions, suggesting that Nar1 was expressed at sufficient levels in strain JAM1T before the inoculation of the oxic and anoxic cultures to carry reduction with no lag phase. Transcriptomic analysis revealed that each strain had distinct relative gene expression profiles, and oxygen had high impact on these profiles. Among denitrification genes and regulatory genes, the nnrS3 gene encoding factor involved in NO-response function had its relative gene transcript levels 5 to 10 times higher in strain GP59 cultured under oxic conditions with than those in both strains cultured under oxic conditions without . Since NnrS senses NO, these results suggest that strain GP59 reduced to NO under oxic conditions, but because of the oxic environment, NO is oxidized back to by flavohemoproteins (NO dioxygenase; Hmp), explaining why reduction is not observed in strain GP59 cultured under oxic conditions. Understanding how these two strains manage the regulation of the denitrification pathway provided some clues on how they response to environmental changes in the original biofilm community, and, by extension, how this community adapts in providing efficient denitrifying activities.

Differential expression of the yfj operon in a Bacillus subtilis biofilm.

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

The effect of urbanization on planktonic and biofilm bacterial communities in different water bodies of the Danube River in Hungary

Freshwaters play an essential role in providing ecosystem services worldwide, however, the water quality of different water bodies is strongly influenced by human activities such as urbanization, industry and agriculture. In this study, water and biofilm samples were collected from the main channel of the Danube River upstream and downstream of a metropolitan, from a regulated side arm within an urbanized area, and from two differently separated oxbow lakes located in nature conservation areas. The taxonomic diversity of bacterial communities was revealed by 16S rRNA gene-based amplicon sequencing using Illumina MiSeq platform. The results showed that all samples were dominated by phyla Pseudomonadota, Actinobacteriota and Bacteroidota. The bacterial community structures, however, clearly differentiated according to planktonic and epilithic or epiphytic habitats, as well as by riverine body types (main channel, side arm, oxbow lakes). The taxonomic diversity of biofilm communities was higher than that of planktonic ones in all studied habitats. Human impacts were mainly reflected in the slowly changing biofilm composition compared to the planktonic ones. Genera with pollution tolerance and/or degradation potential, such as Acinetobacter, Pseudomonas and Shewanella were mainly detected in biofilm communities of the highly urbanized section of the river side arm.

Phage communities in household-related biofilms correlate with bacterial hosts

The average American spends 93% of their time in built environments, almost 70% of that is in their place of residence. Human health and well-being are intrinsically tied to the quality of our personal environments and the microbiomes that populate them. Conversely, the built environment microbiome is seeded, formed, and re-shaped by occupant behavior, cleaning, personal hygiene and food choices, as well as geographic location and variability in infrastructure. Here, we focus on the presence of viruses in household biofilms, specifically in showerheads and on toothbrushes. Bacteriophage, viruses that infect bacteria with high host specificity, have been shown to drive microbial community structure and function through host infection and horizontal gene transfer in environmental systems. Due to the dynamic environment, with extreme temperature changes, periods of wetting/drying and exposure to hygiene/cleaning products, in addition to low biomass and transient nature of indoor microbiomes, we hypothesize that phage host infection in these unique built environments are different from environmental biofilm interactions. We approach the hypothesis using metagenomics, querying 34 toothbrush and 92 showerhead metagenomes. Representative of biofilms in the built environment, these interfaces demonstrate distinct levels of occupant interaction. We identified 22 complete, 232 high quality, and 362 medium quality viral OTUs. Viral community richness correlated with bacterial richness but not Shannon or Simpson indices. Of quality viral OTUs with sufficient coverage (614), 532 were connected with 32 bacterial families, of which only Sphingomonadaceae, Burkholderiaceae, and Caulobacteraceae are found in both toothbrushes and showerheads. Low average nucleotide identity to reference sequences and a high proportion of open reading frames annotated as hypothetical or unknown indicate that these environments harbor many novel and uncharacterized phage. The results of this study reveal the paucity of information available on bacteriophage in indoor environments and indicate a need for more virus-focused methods for DNA extraction and specific sequencing aimed at understanding viral impact on the microbiome in the built environment.

Redox potential shapes spatial heterogeneity of mixed-cultured electroactive biofilm treating wastewater

The core of bioelectrochemical systems (BESs) is electrochemically active microorganisms (EAMs), which exert spatial heterogeneity on electrode surface and influences BESs performance. Setting an optimal potential is an effective strategy for improving and optimizing BESs performance, however, how the electrode potential affects spatial structure of microbial community within anode biofilm is not known. Using a complex substrate-fed BES with a wastewater inoculum, this study investigated the community structure and composition of the stratified biofilm developed under the potential of −0.3 V, 0 V, +0.3 V and +0.6 V (vs. saturated calomel electrode) by freezing microtome method and high-throughput sequencing analysis. The spatial heterogeneity of biofilm community was found to be dependent on the electrode potential and a less-stratified community structure was observed for +0.6 V than other potentials. Within the biofilms, the inner layers selected more Geobacter and the outer layers enriched more Acinetobacter and Serratia, potentially suggested a stratification of electron transfer pathway and metabolite-based interspecies communications. The results demonstrated the response of spatial heterogeneity of anode biofilm community to the change of electrode potential, which help to understand the selective and enrichment of kinetically efficient anodic microbiome by electron potential.

Chlormequat inhibits Vallisneria natans growth and shapes the epiphytic biofilm microbial community.

Submerged macrophytes can overgrow and negatively affect freshwater ecosystems. This study aimed to investigate the use of chlormequat (CQ) to regulate submerged Vallisneria natans growth as well as its impact on the microbial community of epiphytic biofilms. V.natans height under CQ dosages of 20, 100, and 200 mg/L decreased within 21 days by 12.57%, 30.07%, and 44.62%, respectively, while chlorophyll content increased by 1.94%, 20.39%, and 38.83%. At 100 mg/L, CQ reduced the diversity of bacteria in the biofilm attached to V.natans leaves but increased the diversity of the eukaryotic microbial community. CQ strongly inhibited Cyanobacteria; compared with the control group, the treatment group experienced a significant reduction from 36.54% to 2.61%. Treatment significantly inhibited Gastrotricha and Rotifera, two dominant phyla of eukaryotes in the leaf biofilm, reducing their relative abundances by 17.41% and 6.48%, respectively. CQ significantly changed the leaf biofilm microbial community correlation network. The treatment group exhibited lower modularity (2.012) compared with the control group (2.249); however, the central network of the treated group contained a higher number of microbial genera (13) than the control group (4), highlighting the significance of eukaryotic genera in the network. The results obtained from this study provide invaluable scientific context and technical understanding pertinent to the restoration of submerged macrophytes within aquatic ecosystems. PRACTITIONER POINTS: Chlormequat reduced the plant height but increased leaf chlorophyll content. Chlormequat reduced biofilm bacterial diversity but increased eukaryotic diversity. Chlormequat affected the bacterial-fungal association networks in biofilms.

Biofilm formation dynamics in long-distance water conveyance pipelines: Impacts of nutrient levels and metal stress

Biofilm formation in long-distance water conveyance pipelines poses significant risks to water quality, particularly under varying nutrient levels and heavy metal stress. However, the impacts of pipeline material on biofilm formation dynamics under different raw water conditions remain elusive. This study investigated the effects of nutrient availability and Fe-Mn stress on biofilm development, structural stability, bacterial community composition, and the occurrence of viable but non-culturable (VBNC) bacteria. Using reactors with different nutrient conditions, we observed that increased nutrient levels promote biofilm growth but lead to greater instability, heightening the risk of secondary contamination. Notably, nutrient escalation beyond a critical threshold had a diminishing impact on biofilm community composition. Additionally, Fe-Mn stress, while initially enhancing microbial adhesion and metabolic activity, ultimately inhibited biofilm formation over time and increases the prevalence of VBNC bacteria, particularly on stainless steel (SS) surfaces. Our findings also highlighted the importance of material selection for pipelines, with polyvinyl chloride (PVC) showing reduced biofilm formation compared to SS, making it a more suitable option for transporting raw water in environments with high metal content. Dispersal limitation determined the bacterial community assembly during the biofilm formation, accounting for 64.53–90.67 % of the variability in different scenarios. These insights offer valuable guidance for managing biofilm-related issues in water distribution systems, emphasizing the need for careful control of nutrient levels and material choice to ensure water safety over long distances.

Patterns of Biofilm Formation by Members of Listeria, Salmonella, and Pseudomonas at Various Temperatures and the Role of Their Synergistic Interactions in the Formation of Biofilm Communities

Patterns of Biofilm Formation by Members of Listeria, Salmonella, and Pseudomonas at Various Temperatures and the Role of Their Synergistic Interactions in the Formation of Biofilm Communities

Spatial variability of bacterial biofilm communities in a wastewater effluent-impacted suburban stream ecosystem.

Streams in arid and semi-arid biomes are often dependent on their flow from municipal sources, such as wastewater effluent. However, wastewater has been shown to contain high concentrations of nutrients and chemical pollutants that can potentially harm aquatic ecosystems and their biota. Understanding if and the type of microorganisms that respond to pollution sources, specifically effluent from wastewater treatment facilities, in regions where flow is predominantly from treatment facilities, is critical for developing a predictive monitoring approach for eutrophication or other ecological degradation states for freshwaters.

Peri-Implantitis-Associated Microbiota before and after Peri-Implantitis Treatment, the Biofilm “Competitive Balancing” Effect: A Systematic Review of Randomized Controlled Trials

This systematic review of RCTs aimed to characterize short- and long-term changes in peri-implantitis-associated microbiota (total biofilm microbial load and predominant pathogens’ counts) following (any) peri-implantitis treatment in systemically healthy, non-smoking, partially/totally edentulous adults. The study protocol, compliant with the PRISMA statement, was registered on PROSPERO (CRD42024514521) before the literature search. Data from 11 RCTs, assessed through the ROBINS-2 tool, were qualitatively synthesized. No data were retrieved on total edentulism, healthy peri-implant/periodontal sites, treated mucositis, gingivitis, and periodontitis sites. Shortly after treatment, Prevotella intermedia, Fusobacterium nucleatum, and Peptostreptococcus micros prevailed, indicating early colonization, as after implant placement. After both surgical and non-surgical approaches, although not eradicated, the peri-implant total biofilm load, red- and orange-complex species, and Aggregatibacter actinomycetemcomitans counts generally decreased for up to about three months. However, one month after treatment, red-complex species and Prevotella intermedia increased, likely due to persistent tissue-invasive bacteria, unresolved pathological conditions (high probing depth values) favoring anaerobiosis and dysbiosis, and a qualitatively and quantitatively decreased biofilm community, competing and balancing the predominant pathogens (biofilm “competitive balancing” effect), thus allowing recolonization by more virulent bacteria. Red-complex bacteria gradually leveled off to baseline at the six- and twelve-month follow-ups. Fusobacterium nucleatum remained almost unchanged after treatment.

Klebsiella pneumoniae AI-2 transporters mediate interspecies interactions and composition in a three-species biofilm community

Biofilms in nature often exist as communities. In this study, an experimental mixed-species community consisting of Pseudomonas aeruginosa, Pseudomonas protegens and Klebsiella pneumoniae was used to investigate how AI-2 transporters affect interspecies interactions and composition. The K. pneumoniae lsrB/lsrD deletion mutants had a 10–25-fold higher concentration of extracellular AI-2 compared to the wild-type. Although these deletion mutants produced monospecies biofilms of similar biomass, the substitution of these mutants for the parental strain significantly altered composition. Dual-species biofilm assays demonstrated that the changes in composition were due to the cumulative effect of pairwise interactions. It was further revealed that K. pneumoniae being present physically in the consortium was important in AI-2 mediating composition in the consortium, and that AI-2 transporters were crucial in achieving maximum biomass in the community. In conclusion, these findings demonstrate that AI-2 transporters mediate interspecies interactions and is important in maintaining the compositional equilibrium of the community.

Response of bacterial and fungal communities in natural biofilms to bioavailable heavy metals in a mining-affected river

Biofilms, known as “microbial skin” in rivers, respond to rapid and sensitive environmental changes. However, the ecological response mechanisms of bacterial and fungal communities in river biofilms toward heavy metal pollution (HMP) remains poorly understood. This study focused on the key driving factors of bacterial and fungal community diversity and composition and their ecological response mechanisms within periphytic biofilms of Asia's largest Pb–Zn mining area. The diversity, dominant bacterial taxa, and bacteria structure in biofilms were influenced by biologically available heavy metal (HM) fractions, with Ni-F3 (17.96 %) and Pb-F4 (16.27 %) as the main factors affecting the bacterial community structure. Fungal community structure and α-diversity were more susceptible to physicochemical parameters (pH and nutrient elements). Partial least squares path modeling revealed that environmental factors influencing bacterial and fungal communities in biofilms were ranked as water quality > metal fractions > total metals. Dispersal limitation was the most critical ecological process in bacterial (56.9 %) and fungal (73.4 %) assembly. The proportion of heterogeneous selection by bacteria (39.5 %) was higher than that of fungus (26.2 %), which increased with increasing HMP. Bacterial communities had a higher migration rate (0.48) and ecological drift proportion (3.6 %), making them more prone to escape environmental stress. Fungal communities exhibited more keystone species, larger niche width (23.24 ± 13.04 vs. 9.72 ± 5.48), higher organization level, and a more stable co-occurrence network than bacterial communities, which enabled them to better adapt to high environmental pollution levels. These findings expanded the understanding of the spatiotemporal dynamics of microbial communities within biofilms in HM-polluted watersheds and provided new insights into the ecological responses of microbial communities to HMP.

Antibiotics-free compounds for managing carbapenem-resistant bacteria; a narrative review.

Carbapenem-resistant (CR) Gram-negative bacteria have become a significant public health problem in the last decade. In recent years, the prevalence of CR bacteria has increased. The resistance to carbapenems could result from different mechanisms such as loss of porin, penicillin-binding protein alteration, carbapenemase, efflux pump, and biofilm community. Additionally, genetic variations like insertion, deletion, mutation, and post-transcriptional modification of corresponding coding genes could decrease the susceptibility of bacteria to carbapenems. In this regard, scientists are looking for new approaches to inhibit CR bacteria. Using bacteriophages, natural products, nanoparticles, disulfiram, N-acetylcysteine, and antimicrobial peptides showed promising inhibitory effects against CR bacteria. Additionally, the mentioned compounds could destroy the biofilm community of CR bacteria. Using them in combination with conventional antibiotics increases the efficacy of antibiotics, decreases their dosage and toxicity, and resensitizes CR bacteria to antibiotics. Therefore, in the present review article, we have discussed different aspects of non-antibiotic approaches for managing and inhibiting the CR bacteria and various methods and procedures used as an alternative for carbapenems against these bacteria.

Guidelines in Designing a Universal Primer Mixture to Probe and Quantify Antibiotic-Resistant Genes Using the Polymerase Chain Reaction (PCR).

Multidrug resistance efflux pumps (MDREPs) in biofilm communities have become an increasingly expensive problem in clinical settings. Polymerase chain reaction (PCR)-based detection can be used to diagnose and characterize these genes, but this requires effective primer design to minimize false positives and negatives in test conclusions. A universal primer approach has previously been used to detect conserved core genes but not for accessory genes such as MDREPs. This study describes a guideline for the design of primers used in the detection of MDREP genes and an optimization approach for creating primers by using multiple sequence alignments to target conserved regions in silico, progressing from in silico to in vitro to generate working primers. Using thisapproach, this paper was able to generate primers to target sugE, a small multidrug resistance (SMR) protein found in microbial species. Primers were tested positively against synthetic DNA sequences but were inconsistent with DNA extracted from the organism of interest. Primer design informs the shortfalls of this detection technique and the difficulty in characterizing such genomic elements.

Pipe material and natural organic matter impact drinking water biofilm microbial community, pathogen profiles and antibiotic resistome deciphered by metagenomics assembly

Biofilms in drinking water distribution systems (DWDSs) are a determinant to drinking water biosafety. Yet, how and why pipe material and natural organic matter (NOM) affect biofilm microbial community, pathogen composition and antibiotic resistome remain unclear. We characterized the biofilms’ activity, microbial community, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and pathogenic ARG hosts in Centers for Disease Control and Prevention (CDC) reactors with different NOM dosages and pipe materials based on metagenomics assembly. Biofilms in cast iron (CI) pipes exhibited higher activity than those in polyethylene (PE) pipes. NOM addition significantly decreased biofilm activity in CI pipes but increased it in PE pipes. Pipe material exerted more profound effects on microbial community structure than NOM. Azospira was significantly enriched in CI pipes and Sphingopyxis was selected in PE pipes, while pathogen (Ralstonia pickettii) increased considerably in NOM-added reactors. Microbial community network in CI pipes showed more edges (CI 13520, PE 7841) and positive correlation proportions (CI 72.35%, PE 61.69%) than those in PE pipes. Stochastic processes drove assembly of both microbial community and antibiotic resistome in DWDS biofilms based on neutral community model. Bacitracin, fosmidomycin and multidrug ARGs were predominant in both PE and CI pipes. Both pipe materials and NOM regulated the biofilm antibiotic resistome. Plasmid was the major MGE co-existing with ARGs, facilitating ARG horizontal transfer. Pathogens (Achromobacter xylosoxidans and Ralstonia pickettii) carried multiple ARGs (qacEdelta1, OXA-22 and aadA) and MGEs (integrase, plasmid and transposase), which deserved more attention. Microbial community contributed more to ARG change than MGEs. Structure equation model (SEM) demonstrated that turbidity and ammonia affected ARGs by directly mediating Shannon diversity and MGEs. These findings might provide a technical guidance for controlling pathogens and ARGs from the point of pipe material and NOM in drinking water.

A convection-diffusion-reaction system with discontinuous flux modelling biofilm growth in slow sand filters

A Slow Sand Filter (SSF) consists of biofilm attached to saturated packed sand with supernatant water on top, through which water flows by gravity. SSFs are used in the production of drinking water to improve water quality and remove pathogens, and, as they use biological filtration via the microbes present in the biofilm, they are simple and cheap to construct. A drawback of SSFs is that the difficult sampling and the complex dynamics associated with biofilm growth of microbes pose an obstacle for analysis and predictions. In order to overcome this issue, a mathematical model consisting of a non-linear convection-diffusion-reaction system with discontinuous flux is developed from first principles as a unified framework for the dynamics in time and depth of the biofilm and microbial community, where a variety of ecological models can be included in the reaction terms, which also contain attachment, detachment and transfer processes. The multi-phase approach considers three main physical volumes: a biofilm matrix, the water volume enclosed by it and the flowing suspension through the SSF surrounding the biofilm. The only input data needed are the inflow concentrations and rate, light irradiation and temperature. The model includes a Cahn–Hilliard-type equation for the biofilm velocity in the supernatant water. A numerical scheme that preserves physical properties of the solution is also presented. This is achieved with a time-splitting scheme using an upwind scheme with an adaptive time-step size that ensures positivity of the solution under a CFL condition and a reasonable assumption on the separate numerical solution of the Cahn–Hilliard-type equation. The latter is solved numerically with a semi-implicit finite-difference scheme using a mixed form of the equation. The flexible model framework with its numerical scheme allows for including a variety of ecological models, making the investigation and development of increasingly complex simulations possible. Simulations with different model parameters are shown to be qualitatively consistent with the literature.

Flourishing in Darkness: Protist Communities of Water Sites in Shulgan-Tash Cave (Southern Urals, Russia)

Karst caves, formed by the erosion of soluble carbonate rocks, provide unique ecosystems characterized by stable temperatures and high humidity. These conditions support diverse microbial communities, including wall microbial fouling, aquatic biofilms, and planktonic communities. This study discloses the taxonomic diversity of protists in aquatic biotopes of Shulgan-Tash Cave, a culturally significant site and popular tourist destination, by 18S rRNA gene metabarcoding. Our findings reveal the rich protist communities in the cave’s aquatic biotopes, with the highest diversity observed in Blue Lake at the cave entrance. In contrast, Distant Lake in the depth of the cave was inhabited by specific communities of plankton, mats, and pool fingers, which exhibited lower richness and evenness, and were adapted to extreme conditions (cold, darkness, and limited nutrients). High-rank taxa including Opisthokonta, Stramenopiles, and Rhizaria dominated all biotopes, aligning with observations from other subterranean environments. Specific communities of biotopes inside the cave featured distinct dominant taxa: amoeboid stramenopile (Synchromophyceae) and flagellates (Choanoflagellatea and Sandona) in mats; flagellates (Choanoflagellatea, Bicoecaceae, Ancyromonadida) and amoeboid protists (Filasterea) in pool fingers; flagellates (Ochromonadales, Glissomonadida, Synchromophyceae), fungi-like protists (Peronosporomycetes), and fungi (Ustilaginomycotina) in plankton. The specificity of the communities was supported by LEfSe analysis, which revealed enriched or differentially abundant protist taxa in each type of biotope. The predominance of Choanoflagellatea in the communities of cave mats and pool fingers, as well as the predominance of Synchromophyceae in the cave mats, appears to be a unique feature of Shulgan-Tash Cave. The cold-tolerant yeast Malassezia recorded in other caves was present in both plankton and biofilm communities, suggesting its resilience to low temperatures. However, no potentially harmful fungi were detected, positioning this research as a baseline for future monitoring. Our results emphasize the need for ongoing surveillance and conservation efforts to protect the fragile ecosystems of Shulgan-Tash Cave from human-induced disturbances and microbial invasions.