Substrate-restricted methanogenesis and limited volatile organic compound degradation in highly diverse and heterogeneous municipal landfill microbial communities

Discarded diversity: Novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills

Background

Viruses are the most abundant microbial entity on the planet, impacting microbial community structure and ecosystem services. Despite outnumbering Bacteria and Archaea by an order of magnitude, viruses have been comparatively underrepresented in reference databases. Metagenomic examinations have illustrated that viruses of Bacteria and Archaea have been specifically understudied in engineered environments. Here we employed metagenomic and computational biology methods to examine the diversity, host interactions, and genetic systems of viruses predicted from 27 samples taken from three municipal landfills across North America.

Results

We identified numerous viruses that are not represented in reference databases, including the third largest bacteriophage genome identified to date (~678 kbp), and note a cosmopolitan diversity of viruses in landfills that are distinct from viromes in other systems. Host-virus interactions were examined via host CRISPR spacer to viral protospacer mapping which captured hyper-targeted viral populations and six viral populations predicted to infect across multiple phyla. Virally-encoded auxiliary metabolic genes (AMGs) were identified with the potential to augment hosts' methane, sulfur, and contaminant degradation metabolisms, including AMGs not previously reported in literature. CRISPR arrays and CRISPR-Cas systems were identified from predicted viral genomes, including the two largest bacteriophage genomes to contain these genetic features. Some virally encoded Cas effector proteins appear distinct relative to previously reported Cas systems and are interesting targets for potential genome editing tools.

Conclusions

Our observations indicate landfills, as heterogeneous contaminated sites with unique selective pressures, are key locations for diverse viruses and atypical virus-host dynamics.

Global landfill leachate characteristics: Occurrences and abundances of environmental contaminants and the microbiome

Landfill leachates are complex mixtures containing very high concentrations of biodegradable and recalcitrant toxic compounds. Understanding the major contaminant components and microbial community signatures in global landfill leachates is crucial for timely decision-making regarding contaminant management and treatment. Therefore, this study analyzed leachate data from 318 landfill sites primarily used for municipal solid waste disposal, focusing on their chemical and microbiological characteristics. The most prevalent and dominant components in landfill leachates are the chemical oxygen demand (COD, 3.7-75.9 × 103 mg/L) and NH4+ (0.03-0.81 × 104 mg/L), followed by salt species such as SO42- (0.03-5.25 × 103 mg/L), Cl- (3.2-7.8 × 103 mg/L), K+ (0.58-4.20 × 103 mg/L), Na+ (1.3-13.0 × 103 mg/L) and Ca2+ (2.35-230.23 × 103 mg/L), which exhibit significant fluctuations. Heavy metals and metalloids are widely distributed in most landfill leachates but at relatively low concentrations (<182.8 mg/L) compared to conventional parameters. Importantly, there is a distinct global variation in the occurrence of emerging environmental contaminants (ECs). Among these compounds, perfluorooctanoic acid (PFOA, 0.02-7.50 × 103 μg/L) of per- and poly-fluoroalkyl substances (PFAS), bisphenol A (BPA, 0.01-33.46 × 103 μg/L) belonged to endocrine-disrupting compounds (EDCs), together with di-ethyltoluamide (DEET, 1.0-1.0 × 103 μg/L) affiliated to pharmaceuticals and personal care products (PPCPs) are the most frequently detected in landfill leachates. Additionally, the microbial community compositions in most leachates are primarily dominated by Proteobacteria, Bacteroidota, Firmicutes, and Chloroflexi, and some of their abundances are correlated with the concentrations of NH4+, NO3-, Cl-, Na+ and Cr. Notably, the leading microbes driving advanced removal of inorganic nitrogen in the treatment systems are Candidatus Brocadia (anammox), denitrifying Thauera, nitrite-oxidizing bacteria Nitrospira, along with ammonia-oxidizing bacteria Nitrosomonas and Nitrosospira. The findings of this work provide a deeper insight into the leachate characteristics and the sustainable management of landfill leachates, especially presenting a snapshot of the global distribution of pollutants and also the microbiome.

Microbial methane cycling in a landfill on a decadal time scale

Landfills generate outsized environmental footprints due to microbial degradation of organic matter in municipal solid waste, which produces the potent greenhouse gas methane. With global solid waste production predicted to increase substantially in the next few decades, there is a pressing need to better understand the temporal dynamics of biogeochemical processes that control methane cycling in landfills. Here, we use metagenomic approaches to characterize microbial methane cycling in waste that was landfilled over 39 years. Our analyses indicate that newer waste supports more diverse communities with similar composition compared to older waste, which contains lower diversity and more varied communities. Older waste contains primarily autotrophic organisms with versatile redox metabolisms, whereas newer waste is dominated by anaerobic fermenters. Methane-producing microbes are more abundant, diverse, and metabolically versatile in new waste compared to old waste. Our findings indicate that predictive models for methane emission in landfills overlook methane oxidation in the absence of oxygen, as well as certain microbial lineages that can potentially contribute to methane sinks in diverse habitats.

CRISPR-resolved virus-host interactions in a municipal landfill include non-specific viruses, hyper-targeted viral populations, and interviral conflicts

Viruses are the most abundant microbial guild on the planet, impacting microbial community structure and ecosystem services. Viruses are specifically understudied in engineered environments, including examinations of their host interactions. We examined host-virus interactions via host CRISPR spacer to viral protospacer mapping in a municipal landfill across two years. Viruses comprised ~ 4% of both the unassembled reads and assembled basepairs. A total of 458 unique virus-host connections captured hyper-targeted viral populations and host CRISPR array adaptation over time. Four viruses were predicted to infect across multiple phyla, suggesting that some viruses are far less host-specific than is currently understood. We detected 161 viral elements that encode CRISPR arrays, including one with 187 spacers, the longest virally-encoded CRISPR array described to date. Virally-encoded CRISPR arrays targeted other viral elements in interviral conflicts. CRISPR-encoding proviruses integrated into host chromosomes were latent examples of CRISPR-immunity-based superinfection exclusion. The bulk of the observed virus-host interactions fit the one-virus-one-host paradigm, but with limited geographic specificity. Our networks highlight rare and previously undescribed complex interactions influencing the ecology of this dynamic engineered system. Our observations indicate landfills, as heterogeneous contaminated sites with unique selective pressures, are key locations for atypical virus-host dynamics.

1-Butyl-3-methylimidazolium Chloride Affects Anaerobic Digestion through Altering Organics Transformation, Cell Viability, and Microbial Community

1-Butyl-3-methylimidazolium chloride (BmimCl), an imidazolium-based ionic liquid, is considered the representative emerging persistent aquatic pollutant, and its environmental toxicity has attracted a growing concern. However, most of the investigations focused on monocultures or a single organism, with little information available on the complex syntrophic consortium that dominates the complex and successional biochemical processes, such as anaerobic digestion. In this study, the effect of BmimCl at environmentally relevant levels on glucose anaerobic digestion was therefore investigated in several laboratory-scale mesophilic anaerobic digesters to provide such support. Experimental results showed that BmimCl at 1-20 mg/L inhibited the methane production rate by 3.50-31.03%, and 20 mg/L BmimCl inhibited butyrate, hydrogen, and acetate biotransformation by 14.29%, 36.36%, and 11.57%, respectively. Toxicological mechanism studies revealed that extracellular polymeric substances (EPSs) adsorbed and accumulated BmimCl through carboxyl, amino, and hydroxyl groups, which destroyed the EPSs' conformational structure, thereby leading to the inactivation of microbial cells. MiSeq sequencing data indicated that the abundance of Clostridium_sensu_stricto_1, Bacteroides, and Methanothrix decreased by 6.01%, 7.02%, and 18.45%, respectively, in response to 20 mg/L BmimCl. Molecular ecological network analysis showed that compared with the control, the lower network complexity, fewer keystone taxa, and fewer associations among microbial taxa were found in the BmimCl-present digester, indicating the reduced stability of the microbial community.

Insights into leachate reduction in landfill with different ventilation Rates: Balance of Water, waste physicochemical Properties, and microbial community

Ventilation is an efficient approach employed for accelerating stabilization and reducing aftercare of landfill, but its effect on leachate reduction is still elusive. To fill this knowledge gap, five lab-scale landfill reactors with different ventilation rates were established in this study. Suitable ventilation (e.g. 0.25-0.5 L·min^-1·kg^-1 dry solid of waste (DS)) was beneficial to promoting the stabilization of landfill, which effectively accelerated the degradation of organic matter and reduced water content of landfilled waste. Based on the mass balance of water, the dominant input water was initial water of landfilled waste (more than 94 %), which was partially converted to leachate and evaporated water. Ventilation enhanced the intensity of biochemical reactions heat to increase evaporated water content from 0 to 0.29 t/t DS while reducing the leachate generation significantly from 0.69 to 0.49 t/t DS with the increase of ventilation rate. Besides, the hydrophilic substances, such as humic acid-like substances, in landfilled waste increased, and the surface of the landfilled waste converted from smooth to rough. The reduction of the bound water content has a significant correlation with the degradation of organic matter content (p less than 0.05), which reduced the water-holding capacity of waste. Actinobacteriota and Firmicutes were the key bacterial phyla in the degradation of organic matter to promote bio-heat and evaporation of water, thus reducing leachate production under suitable ventilation conditions. Carbohydrates and amino acids were the main energy metabolism sources of bacteria during the landfill process. This study deepens our understanding of the leachate reduction mechanism in the micro-aerobic landfill.