1. Introduction
Ultrafiltration (UF) is an established water treatment process used to retain macromolecular substances, suspended solids and particles. The technology is widely used in many industries, including food and beverage, biotechnology, pharmaceutics and healthcare, but also by mining, chemical or petrochemical companies. In the case of water treatment, its major applications in water treatment are the removal of turbidity, natural organic matter, flocs or microplastic from water [
1,
2]. Especially in water reuse applications, UF is often integrated into the water treatment process [
3]. From a microbiological point of view, ultrafiltration with a typical pore size of 20–30 nm effectively retains bacteria and larger cells [
4], but also most viruses [
5]. The retention rates for bacteria are often stated with at least 6-log units [
6]. As a result, UF can physically disinfect water, thereby providing an important contribution to the hygienization of the corresponding water. A common misconception, however, is that the filtered water is free of microorganisms. While this can apply to fresh filtrates, the treated water typically does not stay free of microbes [
7]. The main reason is that the receiving pipes or water storage compartments are not sterile. Microorganisms are thus reintroduced into the filtered water.
While the majority of UF units serve to treat water on a large scale, small-scale UF systems have been increasingly used in the drinking water installation (DWI) of large buildings to remove unwanted bacteria and particles [
8,
9]. The primary intention when using UF is to increase water quality via particle retention, including the removal of unwanted bacteria like Legionella. The latter goes along with the hope to be able to reduce the hot water temperature [
8], which is intended as a thermal barrier for Legionella. In drinking water installations with central warm water production systems, the temperature is typically set to 60 °C at the exit of hot water boilers [
10]. Being able to reduce the hot water temperature would help reduce the overall energy demand of buildings.
Currently, we lack understanding of the extent of the bacterial regrowth potential after the UF treatment, the sustainability of ultrafiltration and the factors influencing regrowth. Studies have shown that UF membranes efficiently retain particulates (including bacteria) and high-molecular-weight (MW) organic compounds, whereas this does not apply to dissolved low-MW organic compounds [
11]. While the high-MW organic compounds are typically degraded by microorganisms more slowly, the low-MW compounds tend to be easily biodegradable with faster kinetics and constitute the major part of the assimilable organic carbon (AOC) [
11]. It has been shown in laboratory experiments that the extent of the reduction in bacterial regrowth by membrane filtration is thus limited [
7].
In this study, we examined the sustainability of ultrafiltration in real-world applications. The first example comprises small-scale ultrafiltration units placed at the point of entry (POE) of drinking water in drinking water installations (DWI). The questions associated with the ultrafiltration of cold drinking water were about the reductions in cell numbers and regrowth potentials, as well as the sustainability of the effects towards the periphery of the corresponding plumbing systems and over time. Another specific aspect was the effect of UF backflush cycles and cleaning in place (CIP). The second example is from the field of industrial water reuse, addressing the effect of ultrafiltration as part of a treatment process converting whey condensates in a dairy company into high-quality water. The analyses were mostly performed using flow cytometry and were rounded up by high-resolution next-generation sequencing to assess the effect of UF on bacterial communities.
2. Materials and Methods
2.1. Sampling Locations and UF-System
In the case of drinking water installations, UF systems were installed at the POE within the framework of the research project UltraF (BMWK, FKZ 03ET1617A). The corresponding buildings, 1–4, comprised multi-family houses (building 1–3) and a student dormitory (building 4) in different German cities (
Table 1). In all buildings, UF units equipped with multibore
® membranes (inge GmbH, Greifenberg, Germany) with a membrane pore size of 20 nanometers were installed at the point of entry (POE) of the drinking water into the DWI. The drinking water did not contain disinfectant residual.
Building 3 contained a small UF system with a crossflow filtration unit consisting of two filter modules (5 m3/h). It used backwash with filtered water to clean the filter modules. Building 4 contained a large single-filter UF system with dead-end filtration (9.7 m3/h). The cleaning mechanism relied on forward flush with unfiltered water for membrane cleaning.
Reuse samples were collected from a pilot plant located on the production site of a dairy plant in Edewecht (Lower Saxony, Germany), belonging to the dairy company Deutsches Milchkontor (DMK, Edewecht, Germany), within the framework of the EU research project B-WaterSmart (Horizon 2020 grant agreement nr. 869171). The pilot plant was built by Envirochemie GmbH (Rossdorf, Germany) to treat whey vapour condensates resulting from the production of dairy products. The hybrid treatment included both biological and physical treatment. Biological treatment was based on a moving bed bioreactor, a fluidized bed reactor and a multilayer filter [
12]. The subsequent physical treatment included ultrafiltration and reverse osmosis. The hollow fiber UF module (Toray HFUG-2020AN, surface area of 90 m
2) had a pore size of 10 nm and was run in dead-end mode for intervals of 20 to 30 min between backflushes. Samples were taken from the runoff of the multilayer filter (UF feed), the fresh UF filtrate and the effluent of the UF filtrate tank. Samples were taken at four time points over a time period of 13 months. Due to variations in the absolute cell numbers over the optimization of the pilot plant, only the cell numbers for one sampling date (11 December 2023) are shown; however, the overall trends remained the same. Samples for nanopore sequencing were taken on the same sampling date.
2.2. Preparation of AOC-Free Glassware for Regrowth Measurements
An alkaline solution of potassium permanganate was made by separately dissolving (A) 30 g of permanganate (cat.nr. 105082; Merck KGaA, Darmstadt, Germany) and (B) 100 g sodium hydroxide pellets (cat.nr. 106498; Merck KGaA, Darmstadt, Germany) in 500 mL of deionized water each and equilibrated to room temperature. The two solutions were subsequently combined and stored in a 1 L bottle in the dark prior to use. Clean glass vials (50 mL, cat.nr. 7612150; Th. Geyer GmbH & Co.KG, Renningen, Germany) were first washed with deionized water and then filled with this alkaline solution and sealed with appropriate caps (cat. nr. 292401305, DWK Life Sciences, Wertheim, Germany). The entire surface area of the glassware was in contact with the solution. The permanganate solution was decanted (for recycling purposes) and glassware and caps were rinsed three times with tap water and twice with deionized water. Dried glassware and caps were wrapped in aluminum foil. Glassware was heated at 280 °C for at least 8 h or overnight, and caps were heated at 180 °C during that time. Caps were provided with a Teflon seal (special fabrication by Max Werth GmbH Co. KG, Mülheim an der Ruhr, Germany) prior to use. Other glassware was treated accordingly.
2.3. Sample Collection
Samples of the drinking water (potable water cold, PWC) prior and after ultrafiltration were collected directly in 1000 mL sample flasks at the point of (water) entry (POE) in the building, after the UF unit, and additionally at the entry of the drinking water heater in buildings 3 and 4. Furthermore, the 2nd liter of PWC at 2 to 6 different point of use (POU) locations distributed over the entirety of each building (building 1–4) was collected in 1000 mL sample flasks. The sampling procedure included the removal of tap attachments, disinfection and the flushing of the first liter to avoid the sampling of stagnated water. Sampling was performed over a time period of 12 months in buildings 3 and 4, over 21 months in building 1 and over 39 months in building 2.
For regrowth measurements, samples were collected in 250 mL AOC-free glass bottles (Schott AG, Mainz, Germany). Unfiltered drinking water prior to the UF was used as a control. Samples of filtered water were taken directly after the UF and before the entry of the drinking water heater. Samples were taken on three to four different sampling dates spread over approximately three months. The drinking water did not contain any disinfectant. Samples were sent cold over night to the laboratory.
In the case of samples from the dairy company, water volumes of approximately 400 mL were collected in AOC-free borosilicate bottles for flow cytometric analysis. To conserve the microbiological status of the samples and to avoid the loss of cellular viability, samples were transported cold (4 ± 2 °C) to the laboratory and analyzed within 24 h after sampling. For nanopore sequencing, 2 L samples volumes were collected in sterile glassware and transported cold to the laboratory.
2.4. Flow Cytometry
Total cell numbers were quantified using flow cytometry. For this purpose, cells were stained with the fluorescent dye SYBR Green I (10,000 × stock; cat.nr. S-7567; Life Technologies Ltd., Darmstadt, Germany). The dye was diluted to a working stock concentration of 100 × using dimethylsulfoxide (DMSO; Sigma Aldrich, Steinheim am Albuch, Germany) and stored at −20 °C until use. For analysis, aliquots (250 µL) of water samples were transferred into a 96-well plate (cat. nr. 601808, HJ-Bioanalytik GmbH, Erkelenz, Germany). Each sample was analyzed three times (three technical replicates). Water sample aliquots of 200 µL were transferred from this plate into the wells of a second 96-well plate with pre-aliquoted 2 µL of the 100 × SG working stock solution in each well using a 12-channel pipette. The samples and dye solution were thoroughly mixed by pipetting up and down several times. Staining was performed at 37 °C for 13 min in an air incubator. Data was collected using a Novocyte benchtop instrument (ACEA Biosciences Inc., CA, USA) equipped with a 488 nm laser and an autosampler to enable analysis on a 96-well plate basis. Data were analyzed using the instrument-specific NovoExpress
® software (version 1.6.2) and a gating procedure similar to the one described by Gatza et al. [
13]. The settings included an analysis speed of 66 µL/min and the trigger was set to green fluorescence (FITC channel) with a detection threshold of 600 fluorescence units. Ultrapure water supplemented with a bacteriostatic solution (BD Biosciences, NJ, USA) was used as sheath fluid. In the case that the total signals exceeded approximately 5000 signals/sec, water samples were diluted with 0.1 µm of filtered mineral water (Evian, Evian-les-Bains, France). Prior to the measurement of samples, a 0.5% chlorine solution was used to clean the flow cytometric system. The oxidant was removed by subsequently flushing the system for two minutes with filtered Evian water. The cleaning procedure allowed a detection threshold of around 200–2000 cells/mL.
2.5. Assessment of Regrowth Potential
After the quantification of day 0 cell numbers, water samples from the 250 mL sample bottles were split into three 50 mL AOC-free borosilicate glass vials sealed with a cap with Teflon sealant. Vials were filled up to a 20 mL mark. These vials were incubated at 22 °C (±1 °C) for seven days to allow bacterial growth, followed by the repeated flow cytometric assessment of cell numbers. The resulting cell numbers are referred to as day 7 values. In the case of ultrafiltrates, regrowth was caused by autochthonous bacteria that were contained in the filtrates and that presumably originated from the non-sterile surfaces of the receiving filtrate compartments.
2.6. Genomic DNA Extraction and Sequencing
For microbial community analysis of the drinking water, 0.5 L of each sample was filtered through 0.2 µm (0.2 µm polycarbonate filters; Pieper Filter GmbH, Bad Zwischenahn, Germany) using a vacuum manifold. Genomic DNA was extracted using the Aquadien™ DNA Extraction and Purification Kit (cat. nr. 3578121, Bio-Rad Laboratories GmbH, Feldkirchen, Germany). For the drinking water samples, Illumina MiSeq sequencing was performed by Eurofins Genomics (Ebersberg, Germany) after amplifying the V3/4 region of the 16S rRNA gene (467 bp ± 20 bp) using universal primers (forward: 5′-TCGTCGGCAGCGTCAGATGT GTATAAGAGACAGCCTACGGGNGGCWGCAG-3′ and reverse: 5′-GTCTCGTGG GCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC-3′). An insufficient PCR product for sequence analysis was obtained for the sample taken directly after ultrafiltration; therefore, samples from before entry into the drinking water heater (DWH) were used (distance to the UF: approx. 2 m). A sufficient PCR product for sequence analysis could only be obtained in the case of drinking water from building 4 as the drinking water in the other buildings did not contain sufficient bacterial biomass to provide enough PCR product for sequence analysis.
For the treatment of whey vapour condensates, 2 L sample volumes were collected in sterile glassware, transported cold to the laboratory, and filtered using 0.2 µm polycarbonate filters (Pieper Filter GmbH, Bad Zwischenahn, Germany). As in the case of drinking water, insufficient PCR product for sequence analysis was obtained from the sample taken directly after UF filtration. The effluent of the multilayer filter (i.e., UF inflow) was therefore compared with effluent of the UF filtrate tank, which contained higher cell numbers than the fresh filtrate. Genomic DNA was extracted using the FAST DNA SPIN kit from MP Biomedicals. Nanopore sequencing was performed by Biofidus AG (Bielefeld, Germany). Library preparation and sequencing was performed according to the manufacturer’s instructions (SQK-16S114.24, Oxford Nanopore Technologies, Oxford, UK). Sequencing was performed using an R10.4.1 flow cell (FLO-MIN114, Oxford Nanopore Technologies) applying the super-accurate basecalling mode.
2.7. Sequence Analysis
Sequence analysis was performed on the basis of 16S rRNA genes. The sequence analyses of the drinking water samples were performed by the sequencing company Eurofins Genomics (Ebersberg, Germany). In detail, paired-end reads were initially processed using cutadapt [
14] (version 2.7) to remove primer and adapter sequences. As a first step of the microbiome analysis, all reads with ambiguous bases (‘N’) were removed. Chimeric reads were identified and removed based on the de novo algorithm of UCHIME [
15], as implemented in the VSEARCH package [
16]. The remaining set of high-quality reads was processed using minimum entropy decomposition [
17,
18]. Minimum Entropy Decomposition (MED) provides a computationally efficient means of partitioning marker gene datasets into OTUs (Operational Taxonomic Units). Each OTU represents a distinct cluster with significant sequence divergence to any other cluster. By employing Shannon entropy, MED only uses the information-rich nucleotide positions across reads and iteratively partitions large datasets while omitting stochastic variation. The MED procedure outperforms classical, identity-based clustering algorithms. Sequences can be partitioned based on relevant single-nucleotide differences without being susceptible to random sequencing errors. This allows the decomposition of sequence datasets with a single nucleotide resolution. Furthermore, the MED procedure identifies and filters random “noise” in the dataset, i.e., sequences with a very low abundance (less than ≈0.02% of the average sample size). To assign taxonomic information to each OTU, DC-MEGABLAST alignments of cluster-representative sequences to the sequence database were performed. A specific taxonomic assignment for each OTU was then transferred from the set of best-matching reference sequences (lowest common taxonomic unit of all best hits). Hereby, a sequence identity of 70% across at least 80% of the representative sequence was a minimal requirement for considering the reference sequences. The further processing of OTUs and taxonomic assignments was performed using the QIIME software package [
19] version 1.9.1,
http://qiime.org/ (accessed on 14 September 2022). The abundances of bacterial taxonomic units were normalized using the lineage-specific copy numbers of the relevant marker genes to improve estimates [
20]. Shannon–Wiener indices were created for the description of diversity [
21].
For the nanopore sequencing of the whey condensate samples, full-length 16S rRNA gene amplicons were quality-controlled using Filtlong (
https://github.com/rrwick/Filtlong, accessed on 27 May 2024) to a minimum mean quality score of 25 and filtered for size (1200–1650 bp) using a custom awk script. VSEARCH (v2.14.2,
https://github.com/torognes/vsearch, accessed on 27 May 2024) was used to dereplicate quality-controlled reads, which were then aligned to the SILVA 138 reference database (
https://academic.oup.com/nar/article/41/D1/D590/1069277, accessed on 27 May 2024) using minimap2 (v2.17-r941,
https://academic.oup.com/bioinformatics/article/34/18/3094/4994778, accessed on 27 May 2024). The resulting alignments were filtered to retain only those with ≤150 mismatches using a custom awk script and to remove low-quality alignments (mapping quality < 20) with SAMtools (v1.10,
https://academic.oup.com/bioinformatics/article/25/16/2078/204688, accessed on 27 May 2024). Sorted and indexed alignments were then used to extract read clusters, which were matched against the SILVA 138 reference database, generating a sample-specific OTU table with taxonomic annotations. Sample-specific OTU tables were finally concatenated into an abundance matrix, which was then imported into R for processing and visualization.
3. Results
3.1. Cell Numbers and Regrowth Potential of the Microbiome After UF
The effect of UF on cell numbers was assessed using flow cytometry and is shown for two very different applications applying UF to (A) drinking water to protect the drinking water installation (DWI) and (B) to biologically treated whey condensates (B). In the case of the drinking water, UF systems were installed in three different buildings at the point of entry (POE) between the public distribution system and the plumbing system (
Figure 1A). In the case of whey condensates, ultrafiltration was the first membrane treatment step after biological treatment, which consisted of a moving bed bioreactor, a fluidized bed reactor and a multilayer filter (
Figure 1B). Water samples were collected in AOC-free glass bottles and transported cold to the laboratory to conserve the microbiological status at the time point of sampling (day 0).
In the drinking water installation, the total cell counts (TCCs) measured in each building at 3–4 different time points declined, on average, from 75,000 to 110,000 cells/mL at the POE to 800–2700 total cells per mL after the UF treatment, corresponding to a decrease of 97–99% (
Figure 1A). In the case of the biologically treated whey condensate, the total cell counts (TCC
day 0) dropped from 1600.000 to 18,000 cells/mL, corresponding to >99% (
Figure 1B).
After the quantification of day 0 cell numbers, the samples were incubated for seven days at 22 °C to allow the regrowth of the given microbiome on the basis of the assimilable nutrients contained in the corresponding samples. In the case of ultrafiltered drinking water, the TCC increased to 0.7–1.9 × 10
6 cells/mL, representing a 684- to 3600-fold increase (
Figure 1A). The cell numbers in the unfiltered control increased to 1.2–2.0 × 10
6 cells/mL, corresponding to a 11- to 27-fold increase. Therefore, the TCC in the sample after UF and after regrowth reached levels comparable to those of the regrown sample that was not subjected to UF.
In the case of biologically pre-treated whey condensates, the 7-day incubation of the unfiltered sample resulted in a reduction in the cell count from 1.6 × 10
6 to 4.1 × 10
5 TCC/mL (
Figure 1B), probably due to the establishment of a different microbiome. The decrease in cell counts was also observed on other sampling dates. The fresh UF filtrate, on the other hand, showed an increase in cell numbers from 1.8 × 10
4 to 4.9 × 10
5 TCC/mL, corresponding to a 27-fold increase. The subsequent passage of the ultrafiltrate through the filtrate tank typically resulted in a substantial increase in TCC
day 0 (3.3 × 10
5 TCC/mL) and TCC
day 7 values (2.0 × 10
6 TCC/mL). The reason for the increase in TCC
day 0 values lies probably in the migration of surface-bound bacteria into the filtrate, which would suggest that the TCC
day 0 greatly depended on the cleanliness of the filtrate tank. Cleaning prior to sampling typically resulted in lower cell numbers. The increase in the regrowth potential in the filtrate tank, on the other hand, was probably due to the addition of a biodegradable corrosion inhibitor.
Overall, the results corroborate the sufficient availability of dissolved nutrients in the filtrates to support substantial regrowth. The removal of particulates does not have a substantial effect on the regrowth potential. In the following, the focus was on the sustainability of the filtration effect and the influence of the operational conditions of the UF system.
3.2. Effect of UF Dimension and Backwash Frequency on Actual Cell Numbers in Filtrates
To assess the impact of membrane wash cycles and the performance of UF units in real-world applications, two different DWIs equipped with different UF units were compared. The wash frequencies in buildings 3 and 4 were set to 4 h and 24 h, respectively. The UF units in the two buildings furthermore differed in their dimensions. While the UF unit in building 3 consisted of two small filter units and a filtration capacity of 5 m
3/h, the single UF unit in building 4 was substantially larger, with a filtration capacity of 9.7 m
3/h (
Table 1). The two UF systems also differed in their cleaning mechanisms to prevent membranes from clogging and to prevent excessive pressure loss across the membranes. The units in building 3 were cleaned by classical backwash (water flowing in the opposite direction), whereas the unit in building 4 was cleaned by forward flush (water flowing parallel to the membrane in crossflow to loosen the filter cake).
Cell numbers at day 0 were assessed in cold water (potable water cold, PWC) samples from the POE prior to ultrafiltration, directly after the UF unit and at the entrance into a drinking water heater (DWH). The latter served for the production of hot potable water (PWH). Samples were taken at 13 different time points over one full year. The wash frequencies were kept constant during this time period.
In building 3, the cell numbers in PWC samples at the POE varied and ranged between 32,000 and 122,000 TCC/mL (
Figure 2A, left). This variation in cell numbers at the POE occurred over time and corresponds to changes in the cell count of the supplied drinking water and were not affected by the installation of the UF unit. The cell numbers at the sampling point after the UF unit were low, with 6500 TCC/mL at the first time of sampling, and further decreased in the remaining study period to 800–1200 TCC/mL. Compared to the cell numbers at the POE, ultrafiltration resulted in a reduction in cell numbers by 96–99% (
Figure 2A, middle). At the sampling point at the entry of the DWH, the installation of the UF unit resulted in a strong reduction in cell numbers (
Figure 2A, right). While the cell numbers were still slightly elevated seven days after the installation of the UF unit, they became smaller in the following sampling events. Not considering the first sampling event after UF installation, the average reduction in cell numbers at the entry of the DWH accounted for 96% (92–99%). The installation of the UF unit therefore led to a continued decrease in cell numbers over the study time period (
Figure 2A).
The effect of the UF system in the DWI of building 4 was different. This building, a newly constructed dormitory, was equipped with a UF unit prior to the commissioning of the DWI with drinking water. Furthermore, the wash frequency of the large UF system with one membrane filter unit was set to 24 h. The cell numbers in the drinking water at the POE ranged between 6000 and 18,000 cells/mL over the study period (
Figure 2B, left). The highest cell numbers coincided with public holidays, which typically correlated with lower water consumption in the dormitory and therefore increased water age prior to consumption (
Figure 2B, green background). When comparing the cell numbers at the POE with the ones after the UF and prior to the DWH, cell numbers were surprisingly higher after UF than at the POE before filtration in the first sampling rounds (
Figure 2B, middle). The UF in this case did not result in reduced cell numbers. As the membrane integrity was confirmed by pressure tests, it was likely that the higher cell counts after the UF were caused by biofouling on the membrane filtrate site, where the microbiome can proliferate to high cell numbers and release cells into the drinking water. The daily physical wash events by forward flushes can only remove the microorganisms enriched on the feed side, and not the microorganisms growing on the filtrate side of the membrane. Consequently, the UF unit was subjected to a chemical cleaning-in-place (CIP) procedure to remove any biomass on the filtrate side. Only after the CIP did the TCC
day0 levels drop below the ones prior to UF (
Figure 2B, middle). Six days after the CIP, the TCC
day0 reduction corresponded to 63% compared to pre-UF concentrations at the POE. Half a year later, the TCC reduction still accounted for 57–89%; however, the cell reductions did not reach levels of 96–99% after the UF system, as seen in buildings 1–3. A similar tendency could be observed at the entry of the DWH. The measured cell counts at the DWH were, however, slightly higher than directly after UF, indicating regrowth in the DWI (
Figure 2B, right).
Overall, the results indicate that shorter wash frequencies are beneficial for reducing cell numbers in the filtrate. The data also shows the efficiency of a CIP to reduce elevated TCCday 0 values in the filtrate.
3.3. Effect of UF Dimension and Backwash Frequency on Regrowth Potentials in Filtrates
Next, the regrowth potentials in the two buildings were analyzed for DWIs in buildings 3 and 4 in more detail. Whereas the installation of the UF unit in building 3 led to a TCC
day 0 reduction of 97–99% in the filtrate (compared to the unfiltered drinking water,
Figure 2A), the regrowth potentials remained comparable to that of unfiltered drinking water at the POE not only in the fresh filtrate, but also at the entry of the DWH, with an average of 1.9 × 10
6 TCC
day 7/mL (
Figure 3A left). This finding suggested no or only a small effect of UF on regrowth potentials.
In building 4, where the CIP was successful in reducing TCC
day 0 values, the regrowth potential of the ultrafiltered sample was higher than the unfiltered water at the POE (
Figure 3A right). The TCC
day 7 values were thereby subject to some variation over time. At the POE, the regrowth potentials increased over time, averaging 0.3 × 10
6 TCC
day 7/mL, while directly after the UF and at the entry of the DHW, the TCC
day 7 values remained relatively constant, with an average of 0.83 and 0.87 × 10
6 TCC
day 7/mL, respectively. The chemical cleaning in place (CIP) therefore did not change the regrowth potential after the UF (
Figure 3B).
Overall, the regrowth potentials of the drinking water did not undergo a substantial change in any of the two buildings because of ultrafiltration. This indicates that the wash frequency and the CIP influence the actual cell numbers (reflected by TCCday 0 values), but not the regrowth potential of the drinking water.
3.4. Sustainability of the UF Effect Within a DWI
To obtain an insight into the extent of microbial regrowth in drinking water on its way from the ultrafiltration unit into the periphery, we looked at the relative changes in TCC
day 0 values within the DWI of buildings 1–4 over one year. Specifically, the total cell numbers directly after UF and at different points-of-use (POU) sampling sites were compared with the ones in the drinking water at the POE. All buildings were equipped with UF units at the POE. Cell numbers in the POU sampling sites tended to be above those directly after ultrafiltration. In buildings 1–3, the total cell numbers directly after the UF units showed an average reduction of 95% (92–97%) compared to unfiltered drinking water at the POE (
Figure 4). In building 4, after the CIP, an average reduction after the UF of 73% was apparent over the remaining year. The low reduction in TCC observed after the UF is probably due to the persistence of conditions that initially led to membrane biofouling. These conditions remained throughout the study, causing a renewed increase in cell concentrations on the filtrate side of the membrane, particularly during periods of low water consumption (
Figure 4).
For POU samples, taken in the periphery of the DWIs in building 1–3, the reduction in cell numbers amounted, on average, to only 76% compared to the POE. This finding therefore suggested that the cell numbers in drinking water had undergone an average increase of 19% after ultrafiltration during passage through the DWI. In building 4, the reduction in cell numbers at the periphery was only 10% compared to the POE. This indicates that the cell concentrations in the DWI increased by 63% after ultrafiltration. The increase is primarily attributed to extended stagnation periods during holiday breaks, during which higher TCC values were measured compared to periods of regular water usage.
The reason for this increase in the cells concentration is the microbial regrowth within the installation, reducing the effect of ultrafiltration at the POU. In all buildings, the TCC values in the periphery of the DWI showed higher variations than the ones in the proximity of the POE, probably due to varying stagnation times. Overall, the ultrafiltration of drinking water at the house entrance led to substantially lower cell numbers in the drinking water in the periphery, but the UF effect was diminished by regrowth. The extent of regrowth could, however, strongly vary in different buildings (
Figure 4).
3.5. Sustainability of the UF Effect over Time
The observed effect of ultrafiltration on the reduction in the total cell numbers in drinking water was maintained over time at the entrance of the DWH (
Figure 2). The DWH was located in the middle of the DWI. To examine whether this also held true in the periphery of a DWI, we examined the TCC
day 0 values at different POU sampling points over approx. one year. The multifamily building 3 served as an example. After the installation of the UF unit, cell concentrations dropped most significant for the samples taken directly after UF and at the DWH (
Figure 5). The TCC
day 0 values in drinking water sampled at the three different faucets in different bathrooms showed less pronounced reductions, but were significantly below those of the unfiltered drinking water at the POE. The higher cell numbers at the peripheric sampling sites were in line with the increase in cell numbers during passage through the DWI.
Although the effect of ultrafiltration was diminished by regrowth and the UF effect varied between the different POU sampling points, the reduction in cell numbers was sustained over the study time of one year.
3.6. Effect of Ultrafiltration on Bacterial Community Composition
In the next step, we investigated the impact of UF on the composition of bacterial communities. Sequence analysis was conducted for both drinking water (A) and whey vapor condensates (B). A comparison of samples collected before and after UF revealed substantial shifts in bacterial community structures.
For drinking water, the number of detected bacterial families decreased markedly from 72 to 29 following UF treatment. Correspondingly, the Shannon–Wiener diversity index declined from 1.4 at the point of entry to 1.1 after UF (
Figure 6 and
Supplementary Figure S1). At the point of entry, the cold water was dominated by two families: Nitrospiraceae (17.6%) and Thioprofundaceae (14.1%); together, these accounted for 32% of the total bacterial abundance. Other highly abundant families included an unclassified Alphaproteobacteria family (7.4%), Gallionellaceae (5.9%), Caulobacteraceae (3.6%), and Rhodocyclaceae (3.4%). Collectively, these six most abundant families represented 53% of the total community (
Figure 6). After UF, the unclassified Alphaproteobacteria family increased in relative abundance from 7.4% to 19.9%, becoming the most dominant family. Other prominent families included Bdellovibrionaceae (15.1%), Rhodobacteraceae (10.2%), Comamonadaceae (8.6%), Haematococcaceae (6.3%), and Chitinophagaceae (5.8%). Together, these six families accounted for 66% of the total bacterial abundance (
Figure 6).
UF also had a substantial impact on the bacterial community composition in the case of biologically treated whey vapour condensate. Here, the number of detected bacterial families also decreased markedly from 65 to 43 following UF treatment (
Figure 6,
Supplementary Figure S1). The bacterial community in the unfiltered whey condensate was dominated by the two families Oxalobacteraceae (54.3%) and Comamonadaceae (28.1%), which together comprised 82% of the total bacterial abundance. Other abundant families included Spirosomaceae (6.2%), Rhodocyclaceae (2.5%), Chitinophagaceae (2.4%), and Sphingobacteriaceae (1.6%). These six families collectively represented 95% of the total community (
Figure 6). Following UF treatment, the relative abundance of Sphingobacteriaceae increased dramatically from 1.6% to 49.2%, becoming the most dominant family. Additional abundant families included Weeksellaceae (15.5%), Sphingomonadaceae (6.7%), Comamonadaceae (which decreased from 28.1% to 5.9%), Saccharimonadaceae (4.5%), and Oxalobacteraceae (which decreased from 54.3% to 4.3%). These six families together accounted for 86% of the total bacterial abundance (
Figure 6).
These results demonstrate that ultrafiltration caused a profound change in the composition of the bacterial communities. The bacterial populations in the feed and the filtrate were highly distinct. In the case of drinking water, the impact of UF could also be observed in more peripheral sampling sites, meaning that the effect on the microbiome was maintained within the DWI.
4. Discussion
The study addressed the effect of ultrafiltration on cell numbers, regrowth potentials and the microbiome. Examples were presented from two very different applications: drinking water in plumbing systems and water production from whey vapour condensates as a side product of dairy production.
The primary motivation to employ ultrafiltration from a microbiological point of view is to reduce cell numbers. UF membranes typically have bacterial retention efficiencies of at least 6 log-units (i.e., ≥99.9999% [
22,
23]). These are determined based on standardized laboratory protocols. In practice, the quantification of cell numbers by flow cytometry, on the other hand, revealed typical reductions in cell signals that ranged between 91 and 99% (
Figure 1 and
Figure 4); in extreme cases, as in building 4, these were even less. This is in good agreement with another study on a multi-family building in Germany that reported a UF-induced ‘cleaning effect’ of 91% of the TCC [
8]. The discrepancy does, however, not reflect the efficiency of the actual bacterial retention or the integrity of the membranes. The detection of cells in the filtrates rather owes itself to the fact that the filtrate compartments are not sterile. The microorganisms populating the surfaces of these compartments are in equilibrium with the bulk water [
24].
The data indicated that the cell numbers strongly depend on the water usage profile, which determines the time of stagnation. In plumbing systems, the drinking water stagnates on average 23 h per day [
25]. Given time, the bacteria in the drinking water proliferate [
26,
27]. The regrowth kinetics are strongly dependent on the ambient temperature, but in the case of drinking water, weak regrowth can already be detected after overnight stagnation [
26] with peak regrowth occurring from day 4 to day 7 [
7,
27,
28]. This is made possible by the existence of a nutrient basis. Part of those nutrients originate from some of the materials used in plumbing systems. Elastomeric materials like EPDM and other plastic materials are known to promote bacterial growth [
29]. These nutrients add to the regrowth potential that is intrinsic to the corresponding drinking water. In case of drinking waters that originate from treated surface waters, the regrowth potential is primarily caused by oxidative treatment steps like ozonation or chlorine-based disinfection [
28]. Oxidative treatments result in the release of dissolved nutrients that were formerly biologically fixed in form of biomass. Furthermore, oxidative processes lead to a conversion of DOC into AOC by breakdown of complex organic molecules that become more bioavailable [
30]. Regrowth is hereby not limited to drinking water without a disinfection residual (as is the case in this study), but also occurs in plumbing systems receiving drinking water with a secondary disinfectant [
31,
32]. In the case of whey, the contained organic constituents are known to be biodegradable [
33,
34]. These assimilable nutrients are typically dissolved low MW molecules, which are not efficiently retained by ultrafiltration and that can pass membranes unhindered [
11,
35].
The extent of regrowth could strongly vary in different buildings (
Figure 5). Apart from water usage and different materials, regrowth is known to depend on the provided drinking water itself [
28], the size and complexity of the DWI [
36], characteristics of the plumbing system like different pipe diameters (causing different surface to volume ratios [
37] and other conditions specific to the DWI (including temperatures [
38,
39]. Differences in the extent of regrowth within the same building, on the other hand, indicate differences in usage behaviours. In building 3, samples from different peripheral faucets contained different cell numbers at different time points.
Usage behaviour is closely linked to the size of UF units. Over-dimensioned units whose filtration capacity and membrane surface area are not in proportion to water consumption (as is the case in building 4) can lead to increased microbial regrowth and therefore high cell numbers. This is supported by the observed differences in bacterial regrowth between buildings 1 and 4 (
Figure 4). Both buildings significantly varied in size (90 living units in building 1 vs. 30 in building 4), but were equipped with the identical UF unit with a filtration capacity of 9.7 m
3/h. While the total annual PWC consumption in building 1 exceeded 3500 m
3, consumption in building 4 was more than four times lower with approx. 800 m
3. Due to the large dimension of the UF system in regard to the water usage and the lack of continuous daily operation during holiday periods, cell numbers in building 4 increased significantly during those times (
Figure 2B). In contrast, cell numbers after UF in building 1 remained consistently low with minimal variation over time, owing to its permanent operation and the consistently high water consumption in this building (
Figure 4).
Our findings furthermore corroborate that wash frequencies of UF membranes and CIP events have an effect on actual cell numbers in the water. Shorter backwash intervals have been reported to be more effective in mitigating fouling although at increased operational costs [
40]. The accumulation of biomass on the feed side of the filter membranes probably also causes the release of dissolved intracellular nutrients from cells that disintegrate over time. The effect of such ‘nutrient leaching’ across membranes by disintegrating biomass is not well understood, but studies support that the turnover of microorganisms by death (often caused by viral lysis and protozoan grazing) and growth of new microorganisms and the resulting microbial population dynamics is typically greatly underestimated [
41,
42,
43,
44]. Overall, our findings corroborate the importance of the selection of a suitable UF-system dimension with appropriate operational settings to minimize cell numbers in the filtrate. This is not limited to drinking water, but also applies to other areas of use [
45,
46,
47].
Whereas ultrafiltration of water was shown to have only a temporary effect on cell numbers, it profoundly changed the composition of bacterial populations (
Figure 6). This finding supports its effectiveness as a microbial barrier and agrees with reports that regrowth can lead to the establishment of a different microbiome including the risk of hygienically relevant microorganisms [
48]. Differences between the microbiomes in the feed water and the filtrate are not thought to be caused by selective membrane rejection, but by the regrowth of a different bacterial community in the filtrate due to different physical, chemical and biological conditions in the post-UF pipes. Especially the “last meters before the tap” were considered to be most critical for water quality [
49]. Distal ends of building water supplies both harbour the highest cell counts and show most deviations from the municipal water supply microbiome [
31]. The reason could lie in the fact that regrowth is most prominent in the periphery of plumbing systems as it is the end of plumbing lines where water tends to stagnate longest and sees the highest temperatures allowing bacteria to multiply [
50]. Strong regrowth means a greater number of replication cycles and therefore a higher chance that microbial communities evolve in a distinct direction. Ultrafiltration could be seen a means to reinforce this effect due to initially low cell numbers with the concomitant presence of dissolved nutrients. As ultrafiltration results in a strong log-decrease of cell numbers without a substantial effect on the regrowth potential, the resulting high regrowth factors might therefore enhance more dramatic changes of the microbiome over a short distance compared to ‘normal’ regrowth.
The findings underline that the water that was stripped of microorganisms cannot be considered biologically stable [
36,
51]. The barrier function of ultrafiltration leaves the ecological niches unoccupied. In the absence of disinfection residuals, the recolonization with new microorganisms and their subsequent regrowth is thus strongly dependent on the receiving pipes or storage compartments where new microorganisms are introduced. From a hygienic focus, it is important to assure after the ‘microbiological reset’ that the subsequent biological stabilization is based on hygienically safe microbes. The possibility to direct the establishment of a microbiome after the ‘reset’ can be both seen as a chance and a risk. The chance of ultrafiltration lies in the replacement of an undesired microbiome with a favourable one, whereas the risk lies in the establishment of unwanted microorganisms in the biologically unstable water. Biological stabilization of water after ultrafiltration should therefore be considered in critical applications including water reuse. In case of drinking water, biological stabilization can occur through a hygienically safe microbiome associated with the pipe surfaces, whereas in case of industrial applications, passage of UF-filtrates over biological filters might be an option to achieve controlled biological stabilization to minimize the risk of uncontrolled occupation of ecological niches.