Isolation and identification of culturable bacteria, capable of heterotrophic growth, from rapid sand filters of drinking water treatment plants

Cooperative interactions between invader and resident microbial community members weaken the negative diversity-invasion relationship

The negative diversity-invasion relationship observed in microbial invasion studies is commonly explained by competition between the invader and resident populations. However, whether this relationship is affected by invader-resident cooperative interactions is unknown. Using ecological and mathematical approaches, we examined the survival and functionality of Aminobacter niigataensis MSH1 to mineralize 2,6-dichlorobenzamide (BAM), a groundwater micropollutant affecting drinking water production, in sand microcosms when inoculated together with synthetic assemblies of resident bacteria. The assemblies varied in richness and in strains that interacted pairwise with MSH1, including cooperative and competitive interactions. While overall, the negative diversity-invasion relationship was retained, residents engaging in cooperative interactions with the invader had a positive impact on MSH1 survival and functionality, highlighting the dependency of invasion success on community composition. No correlation existed between community richness and the delay in BAM mineralization by MSH1. The findings suggest that the presence of cooperative residents can alleviate the negative diversity-invasion relationship.

Gradual Recovery of Building Plumbing-Associated Microbial Communities after Extended Periods of Altered Water Demand during the COVID-19 Pandemic

COVID-19 pandemic-related building restrictions heightened drinking water microbiological safety concerns post-reopening due to the unprecedented nature of commercial building closures. Starting with phased reopening (i.e., June 2020), we sampled drinking water for 6 months from three commercial buildings with reduced water usage and four occupied residential households. Samples were analyzed using flow cytometry and full-length 16S rRNA gene sequencing along with comprehensive water chemistry characterization. Prolonged building closures resulted in 10-fold higher microbial cell counts in the commercial buildings [(2.95 ± 3.67) × 105 cells mL-1] than in residential households [(1.11 ± 0.58) × 104 cells mL-1] with majority intact cells. While flushing reduced cell counts and increased disinfection residuals, microbial communities in commercial buildings remained distinct from those in residential households on the basis of flow cytometric fingerprinting [Bray-Curtis dissimilarity (dBC) = 0.33 ± 0.07] and 16S rRNA gene sequencing (dBC = 0.72 ± 0.20). An increase in water demand post-reopening resulted in gradual convergence in microbial communities in water samples collected from commercial buildings and residential households. Overall, we find that the gradual recovery of water demand played a key role in the recovery of building plumbing-associated microbial communities as compared to short-term flushing after extended periods of reduced water demand.

Comparative Evaluation of Wild and Farmed Rainbow Trout Fish Based on Representative Chemosensory and Microbial Indicators of Their Habitats

Wild and farmed rainbow trout were compared with chemical profiling, chemosensory properties, carbon concentration and isotope analyses, 1- and 2-GC/O-MS, GC-FID, and aroma profile analyses. Results were linked with the prokaryotic and eukaryotic microbiological profile of the fish sources using multivariate statistical analysis. Fish from natural environments proved to have better sensory properties in terms of fruity, sweet, and citrusy attributes, compared to farmed fish. However, the farmed fish were found to have higher nutritional value based on their lipid contents. These differences might relate to the introduction of feed extrudates, which could influence the overall quality of fish products. Thereby, malodor episodes linked to musty/earthy off-odor notes related to odorants including geosmin, β-caryophyllene, (E,Z)-2,4-nonadienal, and (E,E)-2,4-nonadienal. These compounds, in turn, correlated with Asticcacaulis benevestitus, Curvibacter sp., Albidiferax sp., Aquabacterium commune, and Aquabacterium citratiphilum abundance and were further affected by oxygen levels in the water column.

Possibility of using ionizing radiation treated sludge from drinking water treatment plant as fertilizer in agriculture: Effects of aging

Using ionizing radiation in treating waste sludge from a drinking water treatment plant is a well-known technique. Sludge treated with ionizing radiation can be used as fertilizer in agriculture. In this paper, the effects of aging on the physicochemical characteristics, the content of microorganisms, molds, acrylamide, heavy metal concentration, and total nutrient content in waste sludge treated with e-beam and gamma irradiation were investigated. The possibility of using treated sludge as a fertilizer in agriculture was evaluated. It has been shown that the content of acrylamide in treated sludge after 15 months of storage does not exceed the limits for sludge to be used as fertilizer. If the sludge is stored in closed bags in a dark place, aging does not increase total microorganisms and molds. The research also showed that the sludge's physicochemical characteristics treated in this way do not decrease under the influence of aging. Finally, it has been shown that aging does not change the concentration of heavy metals and total nutrients in sludge treated by ionizing irradiation.

Phage Predation Promotes Filamentous Bacterium Piscinibacter Colonization and Improves Structural and Hydraulic Stability of Microbial Aggregates

Although bacteria-phage interactions have broad environmental applications and ecological implications, the influence of phage predation on bacterial aggregation and structural stability remains largely unexplored. Herein, we demonstrate that inefficient lytic phage predation can promote host filamentous bacterium Piscinibacter colonization onto non-host Thauera aggregates, improving the structural and hydraulic stability of the dual-species aggregates. Specifically, phage predation at 10³-10⁴ PFU/mL (i.e., multiplication of infection at 0.01-0.1) promoted initial Piscinibacter colonization by 10-15 folds and resulted in 29-31% higher abundance of Piscinibacter in the stabilized aggregates than that in the control aggregates without phage predation. Transcriptomic analysis revealed upregulated genes related to quorum sensing (by 15-92 folds) and polysaccharide secretion (by 10-90 folds) within the treated aggregates, which was consistent with 120-172% higher content of polysaccharides for the treated dual-species aggregates. Confocal laser scanning microscopic images further confirmed the increase of filamentous bacteria and polysaccharides (both with wider distribution) within the dual-species aggregates. Accordlingly, the aggregates' structural strength (via atomic force microscopes) and shear resistance (via hydraulic stress tests) increased by 77 and 42%, respectively, relative to the control group. In the long-term experiments, the enhanced hydraulic stability of the treated aggregates could facilitate dwelling bacteria propagation in flow-through conditions. Overall, our study demonstrates that phage predation can promote bacterial aggregation and enhance aggregate structural stability, revealing the beneficial role of lytic phage predation on bacterial symbiosis and environmental adaptivity.

Effects of treatment processes on AOC removal and changes of bacterial diversity in a water treatment plant

The effectiveness of different treatment processes on assimilable organic carbon (AOC) removal and bacterial diversity variations was evaluated in a water treatment plant. The van der Kooij technique was applied for AOC analysis and responses of bacterial communities were characterized by the metagenomics assay. Results show that the AOC concentrations were about 93, 148, 43, 51, 37, and 38 μg acetate-C/L in effluents of raw water basin, preozonation, rapid sand filtration (RSF), ozonation, biofiltration [biological activated carbon (BAC) filtration], and chlorination (clear water), respectively. Increased AOC concentrations were observed after preozonation, ozonation, and chlorination units due to the production of biodegradable organic matters after the oxidation processes. Results indicate that the oxidation processes were the main causes of AOC formation, which resulted in significant increases in AOC concentrations (18-59% increment). The AOC removal efficiencies were 47, 28, and 60% in the RSF, biofiltration, and the whole system, respectively. RSF and biofiltration were responsible for the AOC treatment and both processes played key roles in AOC removal. Thus, both RSF and biofiltration processes would contribute to AOC treatment after oxidation. Sediments from the raw water basin and filter samples from RSF and BAC units were collected and analyzed for bacterial communities. Results from scanning electron microscope analysis indicate that bacterial colonization was observed in filter materials. This indicates that the surfaces of the filter materials were beneficial to bacterial growth and AOC removal via the adsorption and biodegradation mechanisms. Next generation sequencing analyses demonstrate that water treatment processes resulted in the changes of bacterial diversity and community profiles in filters of RSF and BAC. According to the findings of bacterial composition and interactions, the dominant bacterial phyla were Proteobacteria (41% in RSF and 56% in BAC) followed by Planctomycetes and Acidobacteria in RSF and BAC systems, which might affect the AOC biodegradation efficiency. Results would be useful in developing AOC treatment and management processes in water treatment plants.

Water recycle system in an artificial closed ecosystem - Lunar Palace 1: Treatment performance and microbial evolution

Water recycle systems have important implications to realize material circulation in biological regeneration life support systems, which is of significance for long-term space missions and future planetary base. Based on membrane biological activated carbon reactor (MBAR) technologies, the 'Lunar Palace 365' experiment established various treatment processes for condensate wastewater, domestic wastewater, urine, and used nutrient solutions. The 370-day operation data showed the COD_Mn index of purified condensate wastewater decreased to 0.74 ± 0.15 mg/L, which met the standards for drinking water quality. The average removal rate of organic contaminants in domestic wastewater by the MBAR was 85.7% ± 10.2%, and this MBAR also had a stable nitrification performance with effluent NO₃^--N concentrations fluctuating from 145.57 mg/L to 328.59 mg/L. Moreover, the purification of urine achieved the conversion of urea-N to NH₄⁺-N and thus the partial recovery of nitrogen. 16S rDNA sequencing results revealed the evolution of microbial diversity and composition during the long-term operation. Meiothermus, Rhodanobacter, and Ochrobactrum were the dominant microorganisms in various MBARs.

Interspecies Interactions of the 2,6-Dichlorobenzamide Degrading Aminobacter sp. MSH1 with Resident Sand Filter Bacteria: Indications for Mutual Cooperative Interactions That Improve BAM Mineralization Activity

Bioaugmentation often involves an invasion process requiring the establishment and activity of a foreign microbe in the resident community of the target environment. Interactions with resident micro-organisms, either antagonistic or cooperative, are believed to impact invasion. However, few studies have examined the variability of interactions between an invader and resident species of its target environment, and none of them considered a bioremediation context. Aminobacter sp. MSH1 mineralizing the groundwater micropollutant 2,6-dichlorobenzamide (BAM), is proposed for bioaugmentation of sand filters used in drinking water production to avert BAM contamination. We examined the nature of the interactions between MSH1 and 13 sand filter resident bacteria in dual and triple species assemblies in sand microcosms. The residents affected MSH1-mediated BAM mineralization without always impacting MSH1 cell densities, indicating effects on cell physiology rather than on cell number. Exploitative competition explained most of the effects (70%), but indications of interference competition were also found. Two residents improved BAM mineralization in dual species assemblies, apparently in a mutual cooperation, and overruled negative effects by others in triple species systems. The results suggest that sand filter communities contain species that increase MSH1 fitness. This opens doors for assisting bioaugmentation through co-inoculation with "helper" bacteria originating from and adapted to the target environment.

Assessment of the Impact of Temperature on Biofilm Composition with a Laboratory Heat Exchanger Module

Temperature change over the length of heat exchangers might be an important factor affecting biofouling. This research aimed at assessing the impact of temperature on biofilm accumulation and composition with respect to bacterial community and extracellular polymeric substances. Two identical laboratory-scale plate heat exchanger modules were developed and tested. Tap water supplemented with nutrients was fed to the two modules to enhance biofilm formation. One “reference” module was kept at 20.0 ± 1.4 °C and one “heated” module was operated with a counter-flow hot water stream resulting in a bulk water gradient from 20 to 27 °C. Biofilms were grown during 40 days, sampled, and characterized using 16S rRNA gene amplicon sequencing, EPS extraction, FTIR, protein and polysaccharide quantifications. The experiments were performed in consecutive triplicate. Monitoring of heat transfer resistance in the heated module displayed a replicable biofilm growth profile. The module was shown suitable to study the impact of temperature on biofouling formation. Biofilm analyses revealed: (i) comparable amounts of biofilms and EPS yield in the reference and heated modules, (ii) a significantly different protein to polysaccharide ratio in the EPS of the reference (5.4 ± 1.0%) and heated modules (7.8 ± 2.1%), caused by a relatively lower extracellular sugar production at elevated temperatures, and (iii) a strong shift in bacterial community composition with increasing temperature. The outcomes of the study, therefore, suggest that heat induces a change in biofilm bacterial community members and EPS composition, which should be taken into consideration when investigating heat exchanger biofouling and cleaning strategies. Research potential and optimization of the heat exchanger modules are discussed.

Integrating biological As(III) oxidation with Fe(0) electrocoagulation for arsenic removal from groundwater

Arsenic (As) is a toxic element present in many (ground)water sources in the world. Most conventional As removal techniques require pre-oxidation of the neutral arsenite (As(III)) species to the negatively charged arsenate (As(V)) oxyanion to optimize As removal and minimize chemical use. In this work, a novel, continuous-flow As removal system was developed that combines biological As(III) oxidation by bacteria with Fe electrocoagulation (EC), an Fe(0)-based electrochemical technology that generates reactive Fe(III) precipitates to bind As. The bio-integrated FeEC system (bio-FeEC) showed effective oxidation and removal of 150 µg/L As(III), without the need of chemicals. To remove As to below the WHO guideline of 10 µg/L, 10 times lower charge dosage was required for the bio-FeEC system compared to conventional FeEC. This lower Fe dosage requirement reduced sludge production and energy consumption. The As(III) oxidizing biomass was found to consist of bacteria belonging to Comamonadaceae, Rhodobacteraceae and Acidovorax, which are capable of oxidizing As(III) and are common in drinking water biofilms. Characterization of the As-laden Fe solids by X-ray absorption spectroscopy indicated that both bio-FeEC and conventional FeEC produced solids consistent with a mixture of lepidocrocite and 2-line ferrihydrite. Arsenic bound to the solids was dominantly As(V), but a slightly higher fraction of As(V) was detected in the bio-FeEC solids compared to the conventional FeEC.

Microbial communities from subglacial water of naled ice bodies in the forefield of Werenskioldbreen, Svalbard

We assessed the structure of microbial communities in the subglacial drainage system of the Werenskioldbreen glacier, Svalbard, which consists of three independent channels. Dome-shaped naled ice bodies that had been forming and releasing subglacial water in the glacial forefield during accumulations season were used to study glacial microbiome. We tested the hypothesis that the properties of the water transported by these channels are site-dependent and influence bacterial diversity. We therefore established the phylogenetic structure of the subglacial microbial communities using next generation sequencing (NGS) of the 16S rRNA gene and performed bioinformatics analyses. A total of 1409 OTUs (operational taxonomic units) belonged to 40 phyla; mostly Proteobacteria, Gracilibacteria, Bacteroidetes, Actinobacteria and Parcubacteria were identified. Sites located on the edge of Werenskioldbreen forefield (Angell, Kvisla) were mainly dominated by Betaproteobacteria. In the central site (Dusan) domination of Epsilonproteobacteria class was observed. Gracilibacteria (GN02) and Gammaproteobacteria represented the dominant taxa only in the sample Kvisla 2. Principal Coordinate Analysis (PCoA) of beta diversity revealed that phylogenetic profiles grouped in three different clusters according to the sampling site. Moreover, higher similarity of bacterial communities from Angell and Kvisla compared to Dusan was confirmed by cluster analysis and Venn diagrams. The highest alpha index values was measured in Dusan. Richness and phylogenetic diversity indices were significantly (p < .05) and positively correlated with pH values of subglacial water and negatively with concentration of Cl^-, Br^-, and NO₃^- anions. These anions negatively impacted the values of richness indices but positively correlated with abundance of some microbial phyla. Our results indicated that subglacial water from naled ice bodies offer the possibility to study the glacial microbiome. In the studied subglacial water, the microbial community structure was sampling site specific and dependent on the water properties, which in turn were probably influenced by the local bedrock composition.

Guiding Mineralization Co-Culture Discovery Using Bayesian Optimization

Many disciplines rely on testing combinations of compounds, materials, proteins, or bacterial species to drive scientific discovery. It is time-consuming and expensive to determine experimentally, via trial-and-error or random selection approaches, which of the many possible combinations will lead to desirable outcomes. Hence, there is a pressing need for more rational and efficient experimental design approaches to reduce experimental effort. In this work, we demonstrate the potential of machine learning methods for the in silico selection of promising co-culture combinations in the application of bioaugmentation. We use the example of pollutant removal in drinking water treatment plants, which can be achieved using co-cultures of a specialized pollutant degrader with combinations of bacterial isolates. To reduce the experimental effort needed to discover high-performing combinations, we propose a data-driven experimental design. Based on a dataset of mineralization performance for all pairs of 13 bacterial species co-cultured with MSH1, we built a Gaussian process regression model to predict the Gompertz mineralization parameters of the co-cultures of two and three species, based on the single-strain parameters. We subsequently used this model in a Bayesian optimization scheme to suggest potentially high-performing combinations of bacteria. We achieved good performance with this approach, both for predicting mineralization parameters and for selecting effective co-cultures, despite the limited dataset. As a novel application of Bayesian optimization in bioremediation, this experimental design approach has promising applications for highlighting co-culture combinations for in vitro testing in various settings, to lessen the experimental burden and perform more targeted screenings.

Application of sewage sludge to agricultural soil increases the abundance of antibiotic resistance genes without altering the composition of prokaryotic communities

The application of sewage sludge as soil amendment is a common agricultural practice. However, wastewater treatment plants, sewage sludge and sewage sludge-amended soils have been reported as hotspots for the appearance and dissemination of antibiotic resistance, driven, among other factors, by selection pressure exerted by co-exposure to antibiotics and heavy metals. To address this threat to environmental and human health, soil samples from a long-term (24 years) field experiment, carried out to study the impact of thermally dried and anaerobically digested sewage sludge (at different doses and frequencies of application) on agricultural soil quality, were investigated for the presence of genes encoding antibiotic resistance (ARGs) and mobile genetic elements (MGEs). Sewage sludge-induced changes in specific soil physicochemical and microbial properties, as indicators of soil quality, were also investigated. The application of sewage sludge increased the total concentration of copper and zinc in amended soils, but without affecting the bioavailability of these metals, possibly due to the high values of soil pH and organic matter content. Soil microbal quality, as reflected by the value of the Soil Quality Index, was higher in sewage sludge-amended soils. Similarly, the application of sewage sludge increased soil microbial activity and biomass, as well as the abundance of ARGs and MGE genes, posing a risk of dissemination of antibiotic resistance. In contrast, the composition of soil prokaryotic communities was not significantly altered by the application of sewage sludge. We found correlation between soil Cu and Zn concentrations and the abundance of ARGs and MGE genes. It was concluded that sewage sludge-derived amendments must be properly treated and managed if they are to be applied to agricultural soil.

Bacterial growth through microfiltration membranes and NOM characteristics in an MF-RO integrated membrane system: Lab-scale and full-scale studies

Biofilm formation on membrane surfaces causes many operational problems such as a decrease in permeate flux and an increase in hydraulic resistance. In this study, the ability of bacteria to pass through microfiltration (MF) membranes and the growth potential of microfilterable bacteria were investigated in order to understand biofouling in MF-reverse osmosis (RO) integrated membrane systems. Growth of microfilterable bacteria in MF permeate was observed, indicating that not all MF membranes can guarantee the total rejection of bacteria. Changes in natural organic matter (NOM) characteristics and growth potential of bacteria during the treatment process are important factors in the occurrence of biofilm development in water treatment systems. Analysis of protein-like and humic-like substances in NOM of two successive RO stages revealed an increase in the concentrations of both biopolymers and humic substances of RO concentrates. Unexpectedly, the use of antiscalants was seen to enhance the growth of bacteria in the RO feed water in this study. Bacterial 16s rRNA pyrosequencing revealed that passing source water through the MF membranes dramatically changed bacterial community structure. The bacterial communities that passed through the MF steps primarily belonged to the family Comamonadaceae. However, several bacteria groups including Flavobacteriaceae, Sphingobacteriaceae and Sphingomonadaceae selectively composed the biofilm community formed on the RO membranes. Thus, understanding the selectivity and filterability of MF towards microorganisms involved in biofouling on RO membrane surfaces is crucial for the improvement of membrane-related operational processes.

Changes in the Drinking Water Microbiome: Effects of Water Treatments Along the Flow of Two Drinking Water Treatment Plants in a Urbanized Area, Milan (Italy)

While safe and of high quality, drinking water can host an astounding biodiversity of microorganisms, dismantling the belief of its "biological simplicity." During the very few years, we are witnessing an exponential growth in scientific publications, exploring the ecology hidden in drinking water treatment plants (DWTPs) and drinking water distribution system (DWDS). We focused on what happens to the microbial communities from source water (groundwater) throughout the main steps of the potabilization process of a DWTP, located in an urbanized area in Northern Italy. Samples were processed by a stringent water filtration to retain even the smallest environmental bacteria and then analyzed with High-Throughput DNA Sequencing (HTS) techniques. We showed that carbon filters harbored a microbial community seeding and shaping water microbiota downstream, introducing a significant variation on incoming (groundwater) microbial community. Chlorination did not instantly affect the altered microbiota. We were also able to correctly predict (through machine learning analysis) samples belonging to groundwater (overall accuracy was 0.71), but the assignation was not reliable with carbon filter samples, which were incorrectly predicted as chlorination samples. The presence and abundance of specific microorganisms allowed us to hypothesize their role as indicators. In particular, Candidatus Adlerbacteria (Parcubacteria), together with microorganisms belonging to Alphaproteobacteria and Gammaproteobacteria, characterized treated water, but not raw water. An exception, confirming our hypothesis, is given by the samples downstream the filters renewal, which had a composition resembling groundwater. Volatility analysis illustrated how carbon filters represented an ecosystem that is stable over time, probably bearing the environmental conditions that promote the survival and growth of this peculiar microbial community.