Methanogen Community Dynamics and Methanogenic Function Response to Solid Waste Decomposition

Landfill bacteriology: Role in waste bioprocessing elevated landfill gaseselimination and heat management

This study delves into the critical role of microbial ecosystems in landfills, which are pivotal for handling municipal solid waste (MSW). Within these landfills, a complex interplay of several microorganisms (aerobic/anaerobic bacteria, archaea or methanotrophs), drives the conversion of complex substrates into simplified compounds and complete mineralization into the water, inorganic salts, and gases, including biofuel methane gas. These landfills have dominant biotic and abiotic environments where various bacterial, archaeal, and fungal groups evolve and interact to decompose substrate by enabling hydrolytic, fermentative, and methanogenic processes. Each landfill consists of diverse bio-geochemical environments with complex microbial populations, ranging from deeply underground anaerobic methanogenic systems to near-surface aerobic systems. These kinds of landfill generate leachates which in turn emerged as a significant risk to the surrounding because generated leachates are rich in toxic organic/inorganic components, heavy metals, minerals, ammonia and xenobiotics. In addition to this, microbial communities in a landfill ecosystem could not be accurately identified using lab microbial-culturing methods alone because most of the landfill's microorganisms cannot grow on a culture medium. Due to these reasons, research on landfills microbiome has flourished which has been characterized by a change from a culture-dependent approach to a more sophisticated use of molecular techniques like Sanger Sequencing and Next-Generation Sequencing (NGS). These sequencing techniques have completely revolutionized the identification and analysis of these diverse microbial communities. This review underscores the significance of microbial functions in waste decomposition, gas management, and heat control in landfills. It further explores how modern sequencing technologies have transformed our approach to studying these complex ecosystems, offering deeper insights into their taxonomic composition and functionality.

Recent advance of microbial mercury methylation in the environment

Methylmercury formation is mainly driven by microbial-mediated process. The mechanism of microbial mercury methylation has become a crucial research topic for understanding methylation in the environment. Pioneering studies of microbial mercury methylation are focusing on functional strain isolation, microbial community composition characterization, and mechanism elucidation in various environments. Therefore, the functional genes of microbial mercury methylation, global isolations of Hg methylation strains, and their methylation potential were systematically analyzed, and methylators in typical environments were extensively reviewed. The main drivers (key physicochemical factors and microbiota) of microbial mercury methylation were summarized and discussed. Though significant progress on the mechanism of the Hg microbial methylation has been explored in recent decade, it is still limited in several aspects, including (1) molecular biology techniques for identifying methylators; (2) characterization methods for mercury methylation potential; and (3) complex environmental properties (environmental factors, complex communities, etc.). Accordingly, strategies for studying the Hg microbial methylation mechanism were proposed. These strategies include the following: (1) the development of new molecular biology methods to characterize methylation potential; (2) treating the environment as a micro-ecosystem and studying them from a holistic perspective to clearly understand mercury methylation; (3) a more reasonable and sensitive inhibition test needs to be considered. KEY POINTS: • Global Hg microbial methylation is phylogenetically and functionally discussed. • The main drivers of microbial methylation are compared in various condition. • Future study of Hg microbial methylation is proposed.

Antibiotics inhibit methanogenesis during municipal solid waste decomposition

Municipal solid waste (MSW) landfills are significant sources of antibiotics. However, the effects of antibiotics on MSW decomposition process and methanogenesis during solid waste decomposition remain insufficiently characterized. This study investigated the effects of environmentally relevant concentrations (ERCs) of antibiotics (200 μg/kg for each antibiotic) on MSW decomposition and methanogenesis in bioreactors treated with and without eight antibiotics (three tetracyclines, three sulfonamides, and two macrolides). The key phases of MSW decomposition, namely the aerobic, anaerobic acid, and methanogenic phases, were determined by analyzing the key physiochemical parameters of the leachate, including pH, chemical oxygen demand, and biochemical oxygen demand. We assessed the bacterial and archaeal compositions, along with the abundance of the gene encoding the alpha subunit of methyl-coenzyme M reductase (mcrA), during MSW decomposition using high throughput 16S ribosomal RNA (rRNA) gene sequencing and quantitative polymerase chain reactions, respectively. Our results revealed that antibiotics significantly altered the compositions of bacteria and methanogens, leading to decreased mcrA abundance and methanogenesis. Specifically, antibiotics inhibited cellulose-degrading bacteria (Firmicutes) and archaea (E2) in the anaerobic acid phase and hydrolytic bacteria (Proteobacteria) in the methanogenic phase, resulting in lower degradation of biodegradable matter than that of the biodegradation without antibiotics treatment. However, the typical MSW decomposition process indicated by the key decomposition phases was successfully separated in both bioreactors, suggesting that antibiotics did not affect overall MSW decomposition process development or the associated individual decomposition phases establishment. These findings suggest that antibiotics at ERCs may inhibit methanogenesis during MSW decomposition, thereby providing fundamental information for methane management and climate change studies.

Effect of extreme pH conditions on methanogenesis: Methanogen metabolism and community structure

The control of pH is effective for inhibiting methanogenesis in the chain elongation fermentation (CEF) system. However, obscure conclusions exist especially with regard to the underlying mechanism. This study comprehensively explored the responses of methanogenesis in granular sludge at various pH levels, ranging from 4.0 to 10.0, from multiple aspects including methane production, methanogenesis pathway, microbial community structure, energy metabolism and electron transport. Results demonstrated that compared with that at pH 7.0, pH at 4.0, 5.5, 8.5 and 10.0 triggered a 100%, 71.7%, 23.8% and 92.1% suppression on methanogenesis by the end of 3 cycles lasting 21 days. This might be explained by the remarkably inhibited metabolic pathways and intracellular regulations. To be more specific, extreme pH conditions decreased the abundance of the acetoclastic methanogens. However, obligate hydrogenotrophic and facultative acetolactic/hydrogenotrophic methanogens were significantly enriched by 16.9%-19.5 fold. pH stress reduced the gene abundance and/or activity of most enzymes involved in methanogenesis such as acetate kinase (by 81.1%-93.1%), formylmethanofuran dehydrogenase (by 10.9%-54.0%) and tetrahydromethanopterin S-methyltransferase (by 9.3%-41.5%). Additionally, pH stress suppressed electron transport via improper electron carriers and decreased electron amount as evidenced by 46.3%-70.4% reduced coenzyme F₄₂₀ content and diminished abundance of CO dehydrogenase (by 15.5%-70.5%) and NADH:ubiquinone reductase (by 20.2%-94.5%). pH stress also regulated energy metabolism with inhibited ATP synthesis (e.g., ATP citrate synthase level reduced by 20.1%-95.3%). Interestingly, the protein and carbohydrate content secreted in EPS failed to show consistent responses to acidic and alkaline conditions. Specifically, when compared with pH 7.0, the acidic condition remarkably reduced the levels of total EPS and EPS protein while both levels were enhanced in the alkaline condition. However, the EPS carbohydrate content at pH 4.0 and 10.0 both decreased. This study is expected to promote the understanding of the pH control-induced methanogenesis inhibition in the CEF system.

Effects of capping on microbial populations and contaminant immobilization in an old unlined landfill

This research aimed at evaluating the effects of capping on the mitigation of impacts generated by a closed unlined landfill in São Carlos, SP, Brazil. Physicochemical and microbiological analyses (16S rRNA sequencing) of buried solid waste samples were performed, in capped and uncapped areas. Even though leachate pockets could still be encountered in capped areas, the capping construction reduced oxygen availability and created more reducing conditions, propitiating the development of sulfate-reducing bacteria and possibly contributing to the precipitation of the metals Pb, Cd, Ni, Co, As, and Zn as metal sulfides, causing their immobilization. The microbial populations adapted to the anaerobic conditions created under capped zones belonged to the phyla Firmicutes, Chloroflexi, and Euryarchaeota and the genera Methanosaeta, Hydrogenispora, Smithella, and Gelria. Differently, the phyla Acidobacteria, Proteobacteria, Bacteroidetes, and Actinobacteria were more abundant in samples from the uncapped zones, in which the abundance of different genera varied homogeneously. Methanogenic activity was not impaired by the intervention measure, as assessed by the specific methanogenic activity (SMA). Capping of old unlined landfills brings benefits to the immobilization of metals and does not impair microbial degradation, being effective for the mitigation of impacts on soils and water resources.

Impact of incineration slag co-disposed with municipal solid waste on methane production and methanogens ecology in landfills

Co-landfill of incineration slag and municipal solid waste (MSW) is a main method for disposal of slag, and it has the potential of promoting methane (CH₄) production and accelerating landfill stabilization. Four simulated MSW landfill columns loaded with different amount of slag (A, 0%; B, 5%; C, 10%; D, 20%) were established, and the CH₄ production characteristics and methanogenic mechanisms were investigated. The maximum CH₄ concentration in columns A, B, C and D was 10.8%, 23.3%, 36.3% and 34.3%, respectively. Leachate pH and refuse pH were positively correlated with CH₄ concentration. Methanosarcina was the dominant genus with abundance of 35.1%∼75.2% and it was positively correlated with CH₄ concentration. CO₂-reducing and acetoclastic methanogenesis were the main types of methanogenesis pathway, and the methanogenesis functional abundance increased with slag proportion during stable methanogenesis process. This research can help understanding the impact of slag on CH₄ production characteristics and microbiological mechanisms in landfills.

Toward Understanding Microbial Ecology to Restore a Degraded Ecosystem

The microbial community plays an important role in maintaining human health, addressing climate change, maintaining environmental quality, etc. High-throughput sequencing leads to the discovery and identification of more microbial community composition and function in diverse ecosystems. Microbiome therapeutics such as fecal microbiota transplantation for human health and bioaugmentation for activated sludge restoration have drawn great attention. However, microbiome therapeutics cannot secure the success of microbiome transplantation. This paper begins with a view on fecal microbiota transplantation and bioaugmentation and is followed by a parallel analysis of these two microbial therapeutic strategies. Accordingly, the microbial ecology mechanisms behind them were discussed. Finally, future research on microbiota transplantation was proposed. Successful application of both microbial therapeutics for human disease and bioremediation for contaminated environments relies on a better understanding of the microbial "entangled bank" and microbial ecology of these environments.

Microbial Mediation of Carbon, Nitrogen, and Sulfur Cycles During Solid Waste Decomposition

Landfills are a unique "terrestrial ecosystem" and serve as a significant carbon sink. Microorganisms convert biodegradable substances in municipal solid waste (MSW) to CH₄, CO₂, and microbial biomass, consisting of the carbon cycling in landfills. Microbial-mediated N and S cycles are also the important biogeochemical process during MSW decomposition, resulting in N₂O and H₂S emission, respectively. Meanwhile, microbial-mediated N and S cycles affect carbon cycling. How microbial community structure and function respond to C, N, and S cycling during solid waste decomposition, however, are not well-characterized. Here, we show the response of bacterial and archaeal community structure and functions to C, N, and S cycling during solid waste decomposition in a long-term (265 days) operation laboratory-scale bioreactor through 16S rRNA-based pyrosequencing and metagenomics analysis. Bacterial and archaeal community composition varied during solid waste decomposition. Aerobic respiration was the main pathway for CO₂ emission, while anaerobic C fixation was the main pathway in carbon fixation. Methanogenesis and denitrification increased during solid waste decomposition, suggesting increasing CH₄ and N₂O emission. In contract, fermentation decreased along solid waste decomposition. Interestingly, Clostridiales were abundant and showed potential for several pathways in C, N, and S cycling. Archaea were involved in many pathways of C and N cycles. There is a shift between bacteria and archaea involvement in N₂ fixation along solid waste decomposition that bacteria Clostridiales and Bacteroidales were initially dominant and then Methanosarcinales increased and became dominant in methanogenic phase. These results provide extensive microbial mediation of C, N, and S cycling profiles during solid waste decomposition.

Eukaryotic community composition and dynamics during solid waste decomposition

Consortia of microbial community are involved in organic waste decomposition in municipal solid waste (MSW) landfill via competition, syntropy, and predation. Bacterial and archaeal community structure and function have been extensively studied in this process, whereas the eukaryotic community structure and function are largely unidentified. This gap stands for one of the fundamental researches of microbial ecology, that is, "what is the importance of variation in eukaryotic community structure and function to solid waste decomposition? The main idea of this work is to characterize changes in eukaryotic community composition and the associated driver during solid waste decomposition. Using high throughput sequencing targeting 18S rRNA genes, community composition and dynamics of eukaryotic during solid wasted decomposition were studied, as well as the differences with solid waste and leachate physiochemical parameters. Concomitant to the expected changes in physiochemical factors, eukaryotic community composition and diversity changed along solid waste decomposition indicated by aerobic phase (AP), anaerobic acid phase (ACP), and methanogenic phase (MP) and the structure was shaped by the nutrients (BOD₅, total phosphorus, and nitrate) in leachate. Ascomycota, the predominant eukaryote, showed significant (p < 0.05) different structure among AP, ACP, and MP in phylum, genera, and species levels. Abundant Freshwater Opisthokonta was present in MP, suggesting a methane carbon cycling via grazing methane oxidation microorganism. Amoebozoa, Alveolata, Rhizaria, and Stramenopiles showed successional pattern during solid waste decomposition, indicating a short food chain establishment. Characterization on eukaryotic community composition and dynamics during solid waste decomposition are crucial for understanding of microbial consortia ecological function on solid waste decomposition and are also helpful for MSW management.Key points• Abundant Ascomycota significantly differed at AP, ACP, and MP.• Eukaryotic succession indicated a short food chain establishment.• Entire eukaryotic community structure was associated to nutrients in leachate.