2.1. Trickling filter design and operation
To support controlled biofilm growth of hydrogen-oxidizing bacteria (HOB) from tap water, a lab-scale bioreactor with hydrogen and oxygen supply was built (Fig. 1). The reactor was designed as a trickling filter in a PVC column (H = 1 m, Vtotal = 2 L) filled with Kaldnes K1 polyethylene carrier material (Vbed = 1.4 L, specific surface > 900 m²/m³, AnoxKaldnes AB, Sweden) and was operated in a temperature-controlled environment at 20°C. Water was pumped (WM 530s peristaltic pump, Watson Marlow, Belgium) and trickled over the carrier material via a custom-made trickling system with 16 tubes. Gas was added in excess and flowed bottom-up to create a counter current for optimal contact between liquid and gas.
The trickling filter was operated in three subsequent stages. During the first two stages, the trickling filter was operated in batch mode (Q = 0.4 L min− 1, empty bed contact time (EBCT) = Vbed/Q = 3.5 min) where water was recycled from a 10 L DURAN® glass Schott bottle. The first stage was used to rinse the tubing (Tygon® E-3603) and carriers. Demineralized water (8 L, Merck, Belgium) was recycled over the reactor and a recycling vessel for one week, during which the water was replaced every 2 days. In the second stage, biofilm formation on the carrier material was allowed through natural enrichment. During this stage, the recycling vessel was filled with tap water (8 L, Ghent, Belgium) and water was replaced every 2 days for one month. Hereafter, an excess hydrogen and oxygen supply (80 v% H2, 20 v% O2) was connected and tap water was recycled and refreshed every 2 days for one month. Then, the water was weekly refreshed for 5 months.
During the third stage, the reactor was switched to a continuous mode (Q = 0.7 L/h, EBCT = 2 h, 50 v% H2, 50 v% air, Vgas = 600 mL/h). To ensure sufficient gas flow, the total flow was increased after one month of continuous operation (Vgas = 6.3 L/h; 5 v% H2, 95 v% air). The reactor was operated in a steady state for 5 months, with alternating periods of switching the hydrogen supply off (1 × 1 day, 2 × 2 weeks) and back on. During this stage, experimental data was collected through the sampling of the liquid (in- and outlet) and biofilm in periods with and without hydrogen supply. The gas phase composition was checked regularly to confirm the presence of H2 at the in- and outlet.
2.2. Analytical techniques
Liquid effluent samples were filtered using PA syringe filters of 0.22 µm pore size before analysis. Orthophosphate-P (o-PO43−-P) was measured using ion chromatography IC with a standard detection limit of 3.3 µg/L o-PO43−-P. When the measured concentrations were lower, manual peak determination was used to estimate the phosphate concentration (down to levels of 0.03 µg/L o-PO43−-P). Nitrate-N (NO3−-N) was measured using a 930 Compact IC Flex (Metrohm), with chemical suppression and conductivity detector, equipped with a Metrosep A Supp 4/5 Guard/4.0 guard column and a Metrosep A Supp 5- 150/4.0 separation column. Trace elements were determined by inductively coupled plasma mass spectrometry (Perkin Elmer 350D) using 3.6 mL/min He collision gas and 10 µg/L Rh as internal standard. For total organic carbon (TOC) and assimilable organic carbon (AOC) analysis, 40 mL borosilicate glass vials with screw caps containing PTFE-faced liner were used (VWR, Belgium). Glassware was prepared according to Hammes and Egli (2005) to be free of any AOC that may interfere with the measurement. The TOC concentration was measured on the unfiltered samples using a Sievers 900 Portable TOC Analyzer (GE Analytical Instruments, Belgium) in technical quadruplicates. Before each measurement, a manual flush was performed and Milli-Q lab-grade water (Merck, Belgium) was used to check the performance. The AOC concentration was calculated using a flow cytometric assay as described by Hammes and Egli 23. In short, the net cell regrowth (cells mL− 1) after 72 hours is calculated and divided by a theoretical conversion factor of 107 cells µg− 1 AOC. The gas composition was analyzed with a Compact GC4.0 (Global Analyser Solutions, The Netherlands), equipped with a Molsieve 5A pre-column and Porabond Q column (O2, H2, and N2) and an Rt-Q-bond pre-column and column (CO2) and a thermal conductivity detector for volumetric gas composition detection.
2.3. Microbial techniques
Total cell concentrations were measured using an Attune™ NxT flow cytometer (ThermoFisher Scientific, Belgium) with BRxx configuration, equipped with a blue (488 nm, 50mW) and red laser (638 nm, 50mW), seven fluorescence detectors with bandpass filters (BL1: 530/30 nm, BL2: 574/26 nm, BL3: 695/40 nm, BL4: 780/60 nm, RL1: 670/14 nm, RL2: 720/30 nm, RL3: 780/60 nm) and two scatter detectors on the 488 nm laser (FSC: 488/10 nm, SSC: 488/10 nm). The flow cytometer was operated with Attune™ focusing fluid (Thermofisher Scientific, Belgium) as sheath fluid. Samples were stained with SYBR® Green I (SG, 100 x concentrate in 0.22 µm-filtered DMSO, Invitrogen, Belgium) and incubated for 20 minutes at 37°C in the dark before analysis. Then, samples were analysed immediately in triplicate in fixed volume mode at a flow rate of 100 µL/min. Quality control was performed daily using Attune™ performance tracking beads (ThermoFisher Scientific, Belgium).
For 16S rRNA gene sequencing, 250 mL of water was collected in autoclaved glass bottles and filtered through 0.22 µm MCE filters (d = 47 mm, Merck, Belgium) and stored in sterile Petri dishes at -20°C. For biofilm samples, two carriers were added to 2 mL sterile PBS and vortexed, centrifuged at 2500 g for 3 minutes and vortexed again. Then, the carrier material was removed and the PBS with loosened biofilm was added to a DNase- and RNase-free sterile PP vial (Biosigma, Germany), centrifuged for 1 minute at highest speed and supernatant was removed. For representative analyses, the biofilm samples were processed and sequenced in duplicate, and pellets were stored at – 20°C until extraction.
Before extraction, the filters were thawed for 15 minutes, cut (total area of ± 2.73 cm³ per sample) with sterilized scissors and tweezers and added to DNase- and RNase-free sterile PP vials (Biosigma, Germany). Extraction was performed by first mixing the samples with lysis buffer, containing 100 mM Tris (pH 8), 100 mM EDTA (pH 8), 100 mM NaCl, 1% polyvinylpyrrolidone (PVP40) and 2% sodium dodecyl sulphate (SDS). 400 mg of 0.1 mm glass beads was added to the samples after which they were disrupted in a PowerLyzer (Qiagen, The Netherlands) in 5 x 15 s cycles at 4000 rpm with a 45 s second hold. The samples were centrifuged at maximum speed for 5 minutes and the supernatant was added to a new tube containing 500 µL of phenol:chloroform:isoamyl alcohol 25:24:1 at pH 7. After mixing and subsequent centrifugation, the upper phase was added to a new tube containing 700 µl of chloroform. After mixing and centrifugation, 450 µL of the upper phase was added to a new tube containing 500 µL of cold isopropanol and 45 µL of 3 M sodium acetate. The samples were mixed and stored at -20°C for one hour after which they were centrifuged at 4°C for 30 minutes. The supernatant was removed and the DNA pellet dried before dissolving in 50 µL (filters, water samples) or 100 µL (pellets, biofilm samples) of 1 x TE. 10 µL was sent out to LGC genomics GmbH (Germany). Amplicon sequencing of the V3–V4 hypervariable region of the 16S rRNA gene was performed on an Illumina MiSeq platform with v3 chemistry, and the primers 341F (5’-CCT ACG GGN GGC WGC AG -3’) and 785Rmod (5’-GAC TAC HVG GGT ATC TAA KCC-3’) 24.
2.4. Bioassays for regrowth and invasion potential
To avoid carbon contamination, glasswork and pipette tips were rinsed thrice with sterile Milli-Q lab-grade water (Merck, Belgium) when performing the bioassays. The regrowth potential was assessed by taking duplicate samples (10 mL) in sterile borosilicate AOC-free vials (VWR, Belgium), prepared according to Hammes and Egli 23. The vials were incubated at 28°C and 100 rpm in the dark. Samples (200 µL) were taken during a period of six days (day 0, 1, 2, 3, 4 and 6), as it is assumed that growth is completed. The total cell concentration was quantified using flow cytometry. The regrowth potential was calculated relative to the starting concentration using the average cell concentration of technical replicates as described in Eq. 1.
\(\varDelta {regrowth}_{DAY X}=100 \times \frac{avg\left({\frac{cells}{mL}}_{DAY X}\right)-avg\left({\frac{cells}{mL}}_{DAY 0}\right)}{avg\left({\frac{cells}{mL}}_{DAY 0}\right)}\) Eq. 1
The invasion potential was determined using a coliform Lelliottia amnigena strain isolated from a full-scale DWDS in Belgium as a model for unwanted microorganisms in drinking water. The strain was grown (details see SI) and added to water samples (V = 2 L) in a final concentration of 50 cells mL− 1. Samples were taken right before and after addition, and after 2, 4 and 6 hours of incubation at 20°C. The concentration of Lelliottia amnigena was determined by filtering (3 x 50 mL) and incubation (18–22 h, 28°C) on coliforms chromogenic agar (CCA, Carl Roth, Belgium), according to the ISO 9308-1:2014 method for drinking water 25.
2.5. Data analysis and statistics
Amplicon data was processed using the Mothur software package (v.1.44.3) and guidelines 26,27 (details see SI). The data was then imported in R (v. 4.2.0) and further processed using the Phyloseq package (v. 1.40.0). Differential analyses were performed using DESeq2 (v. 1.36.0) based on the Wald significance test and a parametric fit.
Flow cytometric data were extracted as Flow Cytometry Standard (.fcs) files (v. 3.1) and was also processed in R (v. 4.2.0) 28. FlowCore (v. 2.8.0) was used to import the .fcs files 29. A gate was constructed manually and validated visually on the bivariate plot of green versus red fluorescence, bacterial cells were separated from background noise. Cell concentration quantification and fingerprinting was done using Phenoflow (v. 1.1.2) as described by Props et al. 30. Before fingerprinting, FlowAI (v. 1.26.0) was used to check the data quality and to remove anomalous values in terms of flow rate stability, signal acquisition and dynamic range before fingerprinting 31 and the data were resampled to the lowest sample size (n = 14734 cells) to account for size-dependent differences.
Statistical analyses were performed in R (v. 4.2.0) (R Core Team 2020). All hypotheses were tested on the 5% significance level (α = 0.05). Significant differences between groups were checked using the non-parametric pairwise Wilcoxon rank sum test from the stats package (v. 4.2.0) 32. On both the amplicon data and fingerprints, beta diversity was calculated using principal coordinates analysis (PcoA) based on the Bray-Curtis dissimilarity, using vegan (v. 2.6.2) 33. Significant differences in beta diversity were evaluated using PERMANOVA analysis (999 permutations) from the vegan package (v. 2.6.2). Correlations were evaluated using the non-parametric Spearman’s rank correlation test included in the stats package (v. 4.2.0).