3.2.2. Taxonomic analysis at the level of phyla
The analysis at the level of phyla permitted us to observe a clear difference of the samples from capped and uncapped zones (Fig. 5). The exceptions are samples D12 and F12, which may have suffered the same influence of water accumulation in a lower region of the studied area. Additionally, as they were collected in close sites, the specific buried content may have influenced the microbial communities more strongly than the environmental shifts caused by the capping construction.
Firstly, it is important to mention that the phylum Proteobacteria was more abundant in all samples(25–47%), followed by Acidobacteria (9–24%), Chloroflexi (4–14%), Actinobacteria (9–12%), and Firmicutes (3–9%). The phylum Proteobacteria comprehends a great diversity of organisms playing different roles in biochemical processes, both in cleaner and more polluted environments, in closed or active landfills (Morita et al., 2020c; Zainun and Simarani, 2018).
Thus, in the present study it is not possible to associate it with conditions found in capped or uncapped zones, and the phylum was abundant in both conditions. Nevertheless, its lower abundance in capped samples can be associated with its substitution by phyla more adapted to the conditions found in capped zones, such as Chloroflexi, Firmucutes, Euryarchaeota, and DHVEG-6. Those phyla were also abundant in F12, whose specific physicochemical conditions – lower ORP and higher COD and EC values (Figs. 3 and 4) – also may have caused the mentioned substitution.
The phylum Firmicutes has been associated with the hydrolysis of organic matter and correlated with biogas production (Campanaro et al., 2020), and playing important roles in anaerobic and methanogenic phases of organic matter decomposition in landfills (Liu et al., 2019; Song et al., 2015). This agrees with its great representativeness in capped zones, where methanogenesis is more relevant due to the absence of oxygen.
Similarly, representatives of the phylum Chloroflexi are hydrolytic anaerobic bacteria (Qin et al., 2019), being frequently reported in anoxic conditions, acting in the consumption of organic compounds generated by anammox bacteria (Anoxic Ammonia Oxidation) (Kindaichi et al., 2012) and in the degradation of carbohydrates and amino acids in biological reactors (Thiel et al., 2019). It was also dominant in the oxidation of fatty acids during acetogenesis, presenting syntrophy with methanogenic archaea (Saha et al., 2019). Such roles were relevant in the evaluated samples, considering that samples from capped zones presented higher ammonium concentrations and enhanced conditions for methanogenesis.
In this sense, the methanogenic archaea pertain to the phylum Euryarchaeota (Archaea Domain) being strict anaerobes that preserve energy with the production of methane (Madigan et al., 2016). Representatives of such phylum were found to be abundant at reservoir sediments with high metals concentrations (Guo et al., 2019), and at soils with lower pH values and higher water content and ammonium concentrations(Hu et al., 2013). Such phylum was more abundant in samples from capped zones and especially relevant in F12 and D12, where the accumulation of leachate led to higher water content creating anaerobic conditions. Therefore, the similarities found between samples from capped zones and F12 are feasibly associated with ORP conditions, i.e., anaerobic or anoxic conditions in such sites.
Finally, the phylum DHVEG-6 (Deep Sea Hydrothermal Vent Group 6), also abundant in capes areas, is also from the Archaea Domain, being reported in hydrothermal sediments, saline environments, and methanogenic biological reactors treating wastewater. It has been relevant in treatment systems applied to the removal of nitrogen and phosphorus, being favored by environments rich in organic matter and total phosphorus (Fan and Xing, 2016; Kuroda et al., 2014).
In respect of F12, the phyla Ignavibacteriae and Aminicenantes were also abundant in such site. Representatives of Ignavibacteriae are facultative anaerobes, using various electron acceptors, such as nitrite, iron (III), and arsenic (V) (Podosokorskaya et al., 2013). The phylum Aminicenantes, even also encountered in aerobic environments, was more abundant in anaerobic ones (Farag et al., 2014), performing the fermentation of carbohydrates, the anaerobic respiration using nitrite, and acting on the degradation of organic matter in deep aquifers, producing acetate and hydrogen (Kadnikov et al., 2019).
The canonical correlation analysis (CCA, Fig. 6) permitted to clearly observe the phyla Firmicutes, Chloroflexi, and DHVEG-6 in the second quadrant, being represented by samples from the capped zones and suffering influence of the parameters pH, ammonium, and sodium. In the third quadrant, there are the phyla Euryarchaeota, Ignavibacteriae and Aminicenantes, abundant in sample F12 and influenced by the parameters humidity, COD, Ca, and Mg, as well as negatively associated with ORP.
Finally, the phyla Acidobacteria, Proteobacteria, Bacteroidetes, and Actinobacteria abundanant in samples from the uncapped zones, were affected by ORP, phosphate, chloride, and manganese.
3.2.3. Taxonomic analysis at the level of genera
The most abundant genera in all the evaluated samples, independently of their location, were Methylocistis (2.9-5.0%), Anaeromyxobacter (0.9–3.3%), Candidatus Solibacter (0.5–3.5%), e Candidatus Koribacter (0.4–3.5%) (Fig. 7).
Representatives of Methylocistis are methanotrophs, i.e., aerobic methane-oxidizing bacteria, which play important roles in the global cycle of methane, being able to attenuate methane emissions from major sources (Tveit et al., 2019). These organisms are widely distributed in diverse habitats, but most frequently in oxic-anoxic interfaces of methanogenic environments with counter gradients of oxygen, methane and hydrogen (Brune et al., 2000; Hakobyan et al., 2020). Thus, such genus plays an important role in the oxidation of methane and the consequent reduction in the landfill emissions.
Regarding the genus Anaeromyxobacter, it is facultative anaerobe with the ability to reduce various metals such as iron and uranium, dechlorinate aromatic compounds, and perform NO3− reduction (Masuda et al., 2020). Thus, the ability to use different electron acceptors for respiration permits its wide distribution in landfill environments.
Finally, Candidatus Solibacter (0.5–3.5%), e Candidatus Koribacter (0.4–3.5%) were found to be abundant in soil samples from forest and tilled land, showing their wide distribution in natural and disturbed soils (Wiryawan et al., 2022). It’s noticeable that these genera were more abundant in the first layers (samples D11, D21, F11, and F21), showing that their occurrence is feasibly associated with cover and intermediate soil layers.
Differently from those, some genera were found to be more abundant in specific landfill areas. For capped zones, as well as for F12, the most abundant genera were: Hydrogenispora (1.1–1.6% in capped samples and F12, and < 0.1% in other uncapped samples), Methanosaeta (0.3–1.1% in capped samples, 3.7% in F12, and ~ 0.1% in other uncapped samples), Gelria (0.1–0.4% in capped samples, 1.5% in F12, and < 0.04% in other uncapped samples), Smithella (0.1–0.3% in capped samples, 1.3% in F12, and < 0.1% in other uncapped samples), and Spirochaeta 2 (0.6–1.9% in capped samples and F12, < 0.4% in other uncapped samples).
Hydrogenispora (phylum Firmicutes) is composed of bacteria capable of producing butyric acid and H2 (Huang et al., 2019), being abundant in sulfate-reducing environments, in anaerobic sludge (Fang et al., 2020), and in flooded soils, where they are able to survive, possibly due to their ability to produce endospores (Li et al., 2020). This shows that in capped zones and possibly in F12 there is no available oxygen and other electron acceptors, such as sulfate, are used for the degradation of organic matter.
This change in available electron acceptors appears to have been the main factor influencing microbial communities after the intervention measure. It is noteworthy that the use of sulfate with sulfide generation contributes to the precipitation and immobilization of several metals, such as Pb, Cu, Zn and Cd (Costa et al., 2021; Kousi et al, 2011, 2018). In this sense, the detection of high concentrations of sulfate in all samples (Fig. 4) and the microbial shift to anaerobic conditions contribute to the immobilization of such contaminants.
Regarding the genus Methanosaeta, it belongs to the group of methanogenic archaeas, especially to the order Methanosarcinales (Archaea domain) and uses acetate as a substrate for methanogenesis, which is the final step of anaerobic digestion (Madigan et al., 2016). It is an abundant genus not only in anaerobic reactors, but in a diversity of environments such as soils, sediments and contaminated aquifers, being considered the largest producer of methane available on Earth (Rotaru et al., 2014). This genus was found in greater proportion in samples from the capped zone and F12, indicating that appropriate conditions for methanogenesis are found in these environments, i.e., anaerobic environments with by-products of microbial degradation.
Additionally, the genera Methanobacterium, Methanoculleusand Methanosarcina, also belonging to the Archaea domain and frequently found in waste deposits (Campanaro et al., 2020; Song et al., 2015) were also more abundant in capped zones and in F12. Even not shown in Fig. 7 due to their abundance being less than 1%, this occurrence strengthens the influence of oxygen availability on microbial communities from capped zones.
Similarly, the genus Gelria has been reported as in the metabolism of fatty acids, in the final stages of fermentation (Fitzgerald et al., 2019) and in reducing landfill zones with higher organic matter and K content (Morita et al., 2020c). This genus was more abundant in samples located in capped zones and in F12, showing its greater relevance in methanogenic conditions. Since this genus has been associated with anaerobiosis and syntrophy mechanisms (Plugge et al, 2002), it is suggested that the products of its metabolism are substrates for methanogenic archaea.
Another genus commonly associated with syntrophy and which was found in samples from capped zones is Smithella, which has been related to the syntrophic degradation of alkanes, being frequently found in cultures of methanogenic degradation of crude oil (Ji et al., 2020; Wawrik et al., 2016). Oil degradation processes under anaerobic conditions seem to be relevant in the studied landfill, as reported by Pelinson et al. (2020).
Finally, the genus Spirochaeta can be obligate or facultative anaerobic, using carbohydrates as energy and carbon source and being found in aquatic environments and sediments (Paster, 2015). Thus, the anoxic conditions created with the capping construction seem to have favored its growth. Additionally, Pohlschroeder et al. (1994) reported their symbiotic activity with Clostridium species in the degradation of cellulose from leachate; the genus Clostridium is composed of obligatory anaerobic endospore-forming species (Madigan et al., 2016) and was also more abundant in capped zones (especially Clostridium sensu strictu 12, 1, 10, 13, 8, 3 and 1, which were not represented in Fig. 7 because they showed relative abundances lower than 1%).
Differently, the genera Haliangium and Candidatus Methylospira were more abundant in samples from uncapped zones. The genus Haliangium (0.8–1.1% in capped samples and F12, 1.1–2.8% in uncapped samples) is obligate aerobic (Fudou et al., 2002) and Candidatus Methylospira(0.4–0.5% in capped samples, 0.8–2.1% in uncapped samples)is obligate microaerophilic that uses methane as the only source of energy and carbon (Danilova et al., 2016). Thus, the greater availability of oxygen in uncapped zones provided a greater representation of these genera.
Finally, similarly to what was reported by Thakur et al. (2020), the genera not yet classified (“Other”) represented considerable percentages in the sampled points (between 48 and 63%), showing that there is still potential for the discovery of species of biotechnological application in urban solid waste deposits.
The CCA for the predominant genera (Fig. 8) presented an agglomeration of samples from capped zones in the first quadrant. Such aggrupation was represented by the genera Candidatus Koribacter, Candidatus Solibacter, Bacillus and Anaeromyxobacter and influenced by the parameters ORP, ammonium, nitrite, and zinc. Such genera, as previously described, were not distributed in capped areas only, but were located in such quadrant due to their higher relative abundance in such samples. Differently, in uncapped samples there were other locally specific genera with higher abundances, causing such samples to be more homogeneously distributed into the quadrants.
Thus, both the CCA at the level of phyla and genera permitted us to clear observe the differences of microbial populations from capped and uncapped areas. As previously discussed, the capped samples clearly responded to the anaerobic and anoxic conditions created with the capping construction, generating metabolic pathways and syntrophic relations for the degradation of the organic compounds. Consequently, the time lapse of 16 months was considered sufficient for the microbial community to adapt to the new environmental conditions, not being possible to infer that an impairment of the microbial activity occurred. In this regard, the SMA aimed to contribute to this analysis, especially focusing on the methanogenic activity.