3.2. Bacterial Community Abundance and Composition
The analysis of the bacterial sequencing data revealed the presence of 240 amplicon sequence variants (ASVs) of which 157 were identified at the genus level, belonging to 84 identified family taxa, 45 identified order taxa, 24 identified class taxa and 11 phylum taxa.
Clostridiaceae and
Methanotrichaceae were the most abundant for family taxa. Firmicutes were the most abundant phyla, followed by Proteobacteria and Actinobacteria (see
Figure 8). The comparative analysis of the samples made it possible to examine the content of individual taxa over the course of the experiment. Similar results were obtained in studies using the diatomaceous earth/peat (DEP) cell carrier [
17]. Members of Proteobacteria, Chloroflexi and Bacteroidetes are known to have traits related to wastewater treatment [
63]. In addition, Firmicutes are capable to degrade a large range of substrates present in municipal sewage sludge [
14,
17,
37].
Before the WF experiment (WF – control 1), the most abundant were Firmicutes (15.59%) and Proteobacteria (11.32%). The addition of the carrier (WF – Ch/P 1) resulted in an increase in the bacteria from the first group to 74.13% and a decrease in Proteobacteria to 2.08%. After the experiment, the control sample (WF – control 2) remained the richest in Firmicutes (62.57%) and Proteobacteria (6.33%). The amount of bacteria from the phyla Actinobacteria, Bacteroidetes, Campylobacterota, Chloroflexi, Euryarchaeota, Planctomycetes, and Proteobacteria decreased. However, Firmicutes, Synergistetes, and Thermotogae increased during the course of the experiment. The addition of the carrier (WF – Ch/P 2) resulted in increased number of bacteria from taxa Actinobacteria, Bacteroidetes, Chloroflexi, Euryarchaeota, Planctomycetes, and Spirochaetes, when compared to control sample at the same stage of the experiment (WF – control 2). During the course of the experiment, the sample with the carrier (WF – Ch/P 2) consistently maintained the highest amount of Firmicutes bacteria; however, its content decreased to 51.12% compared to the start of the experiment (WF – Ch/P 1). There was, however, an increase in the amount of bacteria of the phylum Euryarchaeota (2.72-fold increase) and Proteobacteria (2.26-fold increase). The correlations described above are similar to the results obtained in studies with both DEP and PLA (polylactide) [
17,
44].
Clostridium was the most abundant genus identified (present in all samples), followed by
Methanothrix (
Figure 5). In each of the experimental layouts,
Clostridium content increased when comparing the sample with the carrier against the control. The same was observed for
Mycobacterium,
Paraclostridium,
Pelolinea, and
Pseudoxanthomonas. The increase in amount of 51 classified genera was observed in WF – ChP 1 sample, 42 in WF – ChP 2 sample, 42 in WFC – ChP 1 sample, and 38 in WFC – ChP 2 sample, in comparison to its control samples. During the course of the experiment, the amount of 43 bacterial genera increased in the WF layout, and 49 in the WFC layout. It is worth mentioning that many sequences unclassified at the genus level were also observed in our research. The highest amount of such ASVs was present in WF – ChP 2 (45.83%) and WF – Control 2 sample (45.05%). In almost all samples, most of unclassified bacteria belonged to Proteobacteria.
Figure 9.
Composition of genus taxa based on the metataxonomic analysis of the 16S rRNA gene.
Figure 9.
Composition of genus taxa based on the metataxonomic analysis of the 16S rRNA gene.
The MetaStat analysis indicated statistically significant differences between the control samples and samples with the addition of the carrier.
Figure 10,
Figure 11,
Figure 12,
Figure 13,
Figure 14 and
Figure 15 show the differences in genus composition between all the analysed samples. For each chart, the number of taxa shown was limited to 30.
A comparative analysis between samples WF – Control 1 and WF – Ch/P 1 showed differences in abundance of 119 taxa (higher content of 47 bacteria in the sample with carrier) (
Figure 10). A lower number of statistically significant differences (81) was found in comparison of WF – Control 2 and WF – Ch/P 2 (
Figure 11).
In WFC - Ch/P 1 sample, a higher amount of 37 bacteria genus was observed, compared to WFC – Control 1 sample. The highest differences were observed for
Trichococcus,
Macellibacteroides,
Lacticaseibacillus,
Longilinea,
Limosilactobacillus,
Falcatimonas,
Pseudobutyrivibrio,
Gemmobacter,
Brevilactibacter,
Uruburuella,
Eubacterium,
Erysipelatoclostridium,
Veillonella,
Enterococcus,
Peptostreptococcus,
Mycobacterium,
Clostridium,
Anaeroarcus,
Desulfobulbus,
Paraclostridium,
Ligilactobacillus, and
Streptococcus (
Figure 12).
Among the 30 bacteria with a higher content in the sample with the addition of the carrier (WFC – Ch/P 2) compared to control sample (WFC – Control 2), the highest significance was found for the following genera:
Dietzia,
Gemmobacter,
Propionicimonas,
Aminobacterium,
Bacillus,
Alcaligenes,
Clostridium,
Mycobacterium,
Paraclostridium,
Acinetobacter,
Paenalcaligenes,
Stenotrophomonas,
Thermomonas,
Tissierella,
Sporosarcina,
Fermentimonas,
Massilibacterium,
Pseudomonas,
Petrimonas, and
Sporanaerobacter (
Figure 13).
Over the course of the experiment, changes occurred that led to the appearance of differences in the content of 72 taxa in the WF samples. More taxa (39), whose abundance was statistically significantly higher, were observed in the sample taken near the final stage of the experiment (WF – Ch/P 2) (
Figure 14). Almost the same observations were made for the WFC experiment (
Figure 15).
The alpha and beta diversity indices calculated from 16S rRNA sequencing data are presented in
Table 5 and
Table 6.
The analysis revealed an abundance of 342 unique bacterial ASVs (Amplicon Sequencing Variants), most of which were present in control samples, and the core microbiome was represented by 291 ASVs (
Figure 15a-f). There were 47 unique ASVs in WF Ch/P 1 sample (
Figure 9a), 32 in WF Ch/P 2 sample (
Figure 9b), 33 in WFC Ch/P 1 sample (
Figure 9c), and 26 in WFC Ch/P 2 sample (
Figure 9d), compared to the control samples. The addition of different carriers resulted in 90 ASVs in the core microbiome at the start of the experiment (
Figure 9e), and 82 ASVs at the end of it (
Figure 9f).
3.3. Physicochemical Analysis of Sludge Samples and Biogas Efficiency
The use of organic substrates of varying composition in waste biogas plants offers the opportunity to achieve high process yields, but also poses limitations related to the need for fermentation monitoring. This allows the process to be controlled and steered. During the decomposition of biomass, especially materials rich in fatty carbohydrates, there can be a rapid release of volatile fatty acids (VFAs) in the first stage, which often results in an acidified environment [
36,
38].
In the case of the experiment presented here, the process was stable, as indicated by the recorded values of the pH parameters, VFA concentration and VFA/TA ratio. Appropriate substrate ratios selected according to the standard [
42], the results of previously performed studies [
35,
37,
41] and the high buffer capacity of the sewage sludge as inoculum provided a guarantee for the successful implementation of the study [
33,
34,
35]. pH values ranging from 6.9 to 7.6 were recorded, where a slight increase in pH occurred for mixtures with added cheese waste as a result of casein decomposition [
36]. VFA concentration was obtained at relatively low values ranging from 1050 mg L
-1 to 1970 mg L
-1, with higher values corresponding to samples with the cosubstrate system and with the addition of carrier. On the other hand, the VFA/TA ratio values were very similar, both for samples with and without carrier, and ranged from 0.26 to 0.43, confirming a stable process [
64].
Quantitative changes in organic matter over time were also measured for in-process samples (from the four bioreactors studied) (see
Figure 17). It was confirmed that during the fermentation of the mixtures studied, there was a loss of organic matter (with the release of biogas), which translated into a decrease in the content of volatile solids in the total solids of the fermented material.
Due to the additional materials applied in the mixtures, a higher content of organic matter was observed in the control samples than in the samples with carrier addition. In the WF variant, a decrease in VS content of approx. 15% was observed, analogously in the control and test sample. In contrast, in the WFC variant, the same difference was approx. 11%, also for both samples. The amount of decomposed organic matter thus depended on the type of substrate rather than the presence of the carrier.
Using samples taken from the bioreactors tested, the rate of changes in organic matter content of the mixtures tested was also analysed (see
Figure 18).
It was found that this parameter was higher for the control samples than for the test samples, which could be related to the addition of carrier to the test samples. At the same time, a higher rate of change was found for the WF variant than for the WFC variant, which could be related to the type of substrate subjected to the fermentation process and is consistent with the greater decrease in VS content in the mixture shown earlier.
Qualitative changes, with respect to the chemical composition of the bioreactors, occurring during the process were investigated using the FT–IR infrared spectroscopy technique and the results obtained are shown in
Figure 19a–d.
When interpreting the accompanying FT-IR spectra, it should be emphasised that the base material of the batches is stabilised sewage sludge (acting as an inoculum), hence the shape of the curves shows great similarity to the spectra of pure sewage sludge. It should also be emphasised that with such a small (yet consistent with the norm for the organic load of an anaerobic bioreactor) proportion of other organic materials (substrates), there could not have been overreaction of the materials. Hence, the spectral shape for all four samples is essentially identical. Differences occur in the size of the characteristic bands, which may indicate different kinetics of decomposition of the individual substances in the bioreactors. The rate of biodegradation may be influenced either by the proportion of carrier or, as inferred earlier (
Figure 18), by the arrangement of the substrates undergoing the process. Both Grube et al., 2006 and Matheri et al., 2020 confirmed that the chemical composition of sewage sludge samples influences the shape of FT–IR spectra, which at the same time has an impact on the degradation process [
65,
66].
Sewage sludge contains mainly proteins, carbohydrates and lipids [
67], however, the digested sludge of carbon compounds may contain considerably less. FT–IR spectra of sewage sludge presented in Figures 19a–d, showed a broad and intense band at 3200-3600 cm
-1, which was attributed to O–H and N–H stretching vibrations. These functional groups confirm the presence of alcohols, carboxylic acids and amides/amines, mainly derived from sewage sludge. The presence of a peak at about 3400 cm
-1 in the dried samples analysed spectroscopically indicates the presence of alcohols, phenols, ethers and acids. This area in the samples exhibited comparable sizes, undergoing some flattening. On the other hand, two further bands appearing at around 2900 cm
-1 and 2800 cm
-1, are particularly prominent at the first sampling dates, as two sharp peaks. These are attributed to asymmetric and symmetric C–H stretching vibrations, respectively, and their shrinkage (indicative of the decomposition of aliphatic chains in carbohydrates and lipids) is particularly observable in Figures 19b,d (samples with the addition of carriers), but least in the control sample with the addition of wafer waste alone. This phenomenon suggests a beneficial effect of combining both the carrier additive and the cosubstrate acting in synergy in the system [
36]. In addition to fat and carbohydrates, which were derived from both inoculum (sludge) and substrates, protein was present in the samples, as indicated by the presence of amide I band and amide II band. These two bands, which gradually disappeared on the spectra of successive terms were recorded at 1650 cm
-1 and 1546 cm
-1, (C=O stretching and N–H bending vibrations). C–O stretching vibrations between 1000 and 1200 cm
-1 confirmed the presence of cellulose, which is a characteristic component of sewage sludge, as noted in their work by Yang et al., 2007 and Pilarska et al., 2019 [
33,
68]. In addition, small peaks of existence between 600 and 900 cm
-1 representing aromatic compounds are observable. The presented characterisation of the spectra is consistent with the literature data [
66,
69]. The shape of the spectra, whose changes occurring during the process are particularly discernible with carbon-related functional groups, indicates the dependence of the degradation rate on both the presence of the carrier and the choice of cosubstrate, where, in the case analysed, the combination of confectionery and cheese waste as a balanced medium for the cells is of particular importance [
36].
The biogas yield results obtained show a positive effect of both the addition of the carrier and the combination of confectionery and dairy waste in the cosubstrate system, which corresponds to the results of the analyses presented above (
Figure 17,
Figure 18 and
Figure 19). For the fermented sample of stand-alone wafer substrates (WF–control and WF–Ch/P), the addition of a cell carrier based on chitosan and perlite (3:1) contributed to a 12.05% increase in biogas/methane generation efficiency (
Table 7). This addition, as an effective support for methanogenic cells, also resulted in an increase in the methane content of the biogas (from 53.2% to 55.5%), indicating an increase in the decomposition rate of organic matter. Combining the cosubstrate used in the system with porous and compatible microbial carriers, gives a definite improvement in process efficiency, as already proved by the results of a study by the same authors [
36]. In the WFC–control and WFC–Ch/P systems, there was a 19.16% increase in process yield, which is very close to the results of studies with silica/lignin carrier (4:1) [
37]. In comparison with other carriers previously tested by the same researchers, the values obtained are comparable or slightly lower [
14,
37]. These include a carrier such as diatomaceous earth/peat (3:1) or granulated PLA (which acted as both a carrier and a medium for the cells). Nevertheless, all, both currently discussed and presented in previous publications, carrier materials are worthy of consideration, due to their properties, favourable impact on process efficiency, affordability and price.
The volume of methane, obtained from the WF–control, in terms of volatile solids (VS) was 351.72 m
3 Mg
-1 VS (see
Table 7) and increased to 411.14 m
3 Mg
-1 VS as a result of the addition of the carrier. The amount of methane obtained from the control cosubstrate sample was greater at 476.84 m
3 Mg
-1 VS. The addition of carrier to the WFC–Ch/P system increased the methane productivity, reaching 518.08 m
3 Mg
-1 VS.