Leachate microbiome profile reveals bacteria, archaea and eukaryote dynamics and methanogenic function during solid waste decomposition

Tracing residual patterns and microbial communities of pharmaceuticals and personal care products from 17 urban landfills leachate in China

Landfill leachate contributes significantly to the presence of pharmaceuticals and personal care products (PPCPs) in the environment, and is a crucial source of contamination. To examine the occurrence of PPCPs and microbial communities, this study comprehensively investigated the concentrations of PPCPs and the abundance of microorganisms in the leachate from 17 municipal landfills across China. Generally, Lidocaine, Linear alkylbenzene sulfonate-C11, and Triclocarban, which are closely associated with human activities, exhibited a detection frequency of 100 % in the leachate. Driven by consumer demand, analgesic and antipyretic drugs have emerged as the most prominent PPCPs in leachate (accounting for 39.9 %). Notably, the Ibuprofen peaked at 56.3 μg/L. Regarding spatial distribution, the contamination of PPCPs in leachates from the eastern regions of China was significantly higher than that in other regions, owing to the level of economic development and demographic factors. Furthermore, the 16S rRNA results revealed significant differences in microbial communities among the leachates from different areas. Although the impact of PPCPs on microbial communities may not be as significant as that of environmental factors, most positive correlations between PPCPs and microorganisms indicate their potential role in providing nutrients and creating favorable conditions for microbial growth. Overall, this research offers new perspectives on the residual features of PPCPs and the microbial community structure in leachates from various regions in China.

A mixed blessing of influent leachate microbes in downstream biotreatment systems of a full-scale landfill leachate treatment plant

In landfill leachate treatment plants (LLTPs), the microbiome plays a pivotal role in the decomposition of organic compounds, reduction in nutrient levels, and elimination of toxins. However, the effects of microbes in landfill leachate influents on downstream treatment systems remain poorly understood. To address this knowledge gap, we collected 23 metagenomic and 12 metatranscriptomic samples from landfill leachate and activated sludge from various treatment units in a full-scale LLTP. We successfully recovered 1,152 non-redundant metagenome-assembled genomes (MAGs), encompassing a wide taxonomic range, including 48 phyla, 95 classes, 166 orders, 247 families, 238 genera, and 1,152 species. More diverse microbes were observed in the influent leachate than in the downstream biotreatment systems, among which, an unprecedented ∼30 % of microbes with transcriptional expression migrated from the influent to the biological treatment units. Network analysis revealed that 399 shared MAGs across the four units exhibited high node centrality and degree, thus supporting enhanced interactions and increased stability of microbial communities. Functional reconstruction and genome characterization of MAGs indicated that these shared MAGs possessed greater capabilities for carbon, nitrogen, sulfur, and arsenic metabolism compared to non-shared MAGs. We further identified a novel species of Zixibacteria in the leachate influent with discrete lineages from those in other environments that accounted for up to 17 % of the abundance of the shared microbial community and exhibited notable metabolic versatility. Meanwhile, we presented groundbreaking evidence of the involvement of Zixibacteria-encoded genes in the production of harmful gas emissions, such as N2O and H2S, at the transcriptional level, thus suggesting that influent microbes may pose safety risks to downstream treatment systems. In summary, this study revealed the complex impact of the influent microbiome on LLTP and emphasizes the need to consider these microbial characteristics when designing treatment technologies and strategies for landfill leachate management.

New insights into antibiotic stimulation of methane production during anaerobic digestion

Residual antibiotics in swine wastewater pose a critical challenge for stable anaerobic digestion (AD). This study offers fresh insights into the anaerobic treatment of swine wastewater. The results showed that the presence of three typical antibiotics (sulfamethoxazole (SMX), oxytetracycline (OTC) and ciprofloxacin (CIP)) in swine wastewater could promote methane production by stimulating the production and conversion of ethanol. Among them, SMX exhibited the strongest methane promotion effect, with the cumulative methane production increasing from 138.47 to 2204.19 mL/g VS. According to the microbial community structure, antibiotics could promote the growth of Corynebacterium, Lutispora and hydrogenotrophic methanogens (Methanosassiliicoccus, Methanobrevibacter, and Methanobacterium), but inhibit the enrichment of acetoclastic methanogen (Methanosaeta). The relative abundance of Methanosaeta decreased from 2.93-19.80% to 0.52-2.58% under antibiotic stress. Furthermore, there were significant differences in the influence of different antibiotic types on methanogenic pathways. Specifically, OTC and CIP promoted the acetoclastic and hydrogenotrophic pathways, respectively, to enhance methane production. However, SMX could promote both acetoclastic and hydrogenotrophic pathways.

Responses of greenhouse gas emissions to aeration coupled with functional membrane during industrial-scale composting of dairy manure: Insights into bacterial community composition and function

Greenhouse gas (GHG) emissions from manure management processes deserve more attention. Using three industrial-scale experiments, this study comprehensively evaluated the effects of different aeration coupled with semi-permeable membrane-covered strategies on the structure and function of bacterial communities and their impact on GHG emissions during dairy manure aerobic composting. The succession of the bacterial communities tended to be consistent for similar aeration strategies. Ruminiclostridium and norank_f__MBA03 were significantly positively correlated with the methane emission rate, and forced aeration coupled with semi-permeable membrane-covered decreased GHG emissions by inhibiting these taxa. Metabolism was the most active function of the bacterial communities, and its relative abundance accounted for 75.69%-80.23%. The combined process also enhanced carbohydrate metabolism and amino acid metabolism. Therefore, forced aeration coupled with semi-permeable membrane-covered represented a novel strategy for reducing global warming potential by regulating the structure and function of the bacterial communities during aerobic composting of dairy manure.

Physiochemical and biological characteristics of fouling on landfill leachate treatment systems surface

Fouling of landfill leachate, a biofilm formation process on the surface of the collection system, migration pipeline and treatment system causes low efficiency of leachate transportation and treatment and increases cost for maintenance of those facilities. In addition, landfill leachate fouling might accumulate pathogens and antibiotic resistance genes (ARGs), posing threats to the environment. Characterization of the landfill leachate fouling and its associated environmental behavior is essential for the management of fouling. In this study, physicochemical and biological properties of landfill leachate fouling and the possible accumulation capacity of pathogens and ARGs were investigated in nitrification (aerobic condition) and denitrification (anaerobic condition) process during landfill leachate biological treatment, respectively. Results show that microbial (bacterial, archaeal, eukaryotic, and viral) community structure and function (carbon fixation, methanogenesis, nitrification and denitrification) differed in fouling under aerobic and anaerobic conditions, driven by the supplemental leachate water quality. Aerobic fouling had a higher abundance of nitrification and denitrification functional genes, while anaerobic fouling harbored a higher abundance of carbon fixation and methanogenesis genes. Both forms of leachate fouling had a higher abundance of pathogens and ARGs than the associated leachate, suggesting the accumulation capacity of fouling on biotic pollutants. Specifically, aerobic fouling harbored three orders of magnitude higher multidrug resistance genes mexD than its associated leachate. This finding provides fundamental knowledge on the biological properties of leachate fouling and suggests that leachate fouling might harbor significant pathogens and ARGs.

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.

Mechanism of antibiotic resistance development in an activated sludge system under tetracycline pressure

The mechanism of antibiotic resistance (AR) development in an activated sludge system under tetracycline (TC) pressure was discussed and analyzed. According to the variation of macro-factors, including TC, COD, TN, TP, NH3-N, pH, heavy metals, and reactor settings, the tet genes respond accordingly. Consequently, the enrichment sites of tet genes form an invisible AR selection zone, where AR microorganisms thrive, gather, reproduce, and spread. The efflux pump genes tetA and tetB prefer anaerobic environment, while ribosome protective protein genes tetM, tetO, tetQ, tetT, and tetW were more concentrated in aerobic situations. As a corresponding micro-effect, different types of tet genes selected the corresponding dominant bacteria such as Thauera and Arthrobacter, suggesting the intrinsic relationship between tet genes and potential hosts. In summary, the macro-response and micro-effect of tet genes constitute an interactive mechanism with tet genes as the core, which is the crucial cause for the continuous development of AR. This study provides an executable strategy to control the development of AR in actual wastewater treatment plants from the perspective of macro-factors and micro-effects.

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.

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.

Viral community in landfill leachate: Occurrence, bacterial hosts, mediation antibiotic resistance gene dissemination, and function in municipal solid waste decomposition

A municipal solid waste (MSW) landfill is a significant source of antibiotic resistance, pathogens and viruses and also a habitat for microbial consortia that perform MSW decomposition. Viruses are of great significance in ecological interactions such as MSW decomposition and antibiotic resistance gene (ARG) transmission. In this study, the viral community structure and the associated driver, the linkage of viruses and their bacterial hosts, the virus-associated ARG dissemination and virtual community function on MSW decomposition were investigated in landfill leachate from seven cities, China. The seven cities include four megacities, two large-scale cities and one small-scale city, representing the leachate characters of China. The results showed that the leachates were dominated by the phage families Siphoviridae, Myoviridae and Podoviridae (91.7 ± 3.6) %. Their putative hosts were the important MSW decomposers Lactobacillus, Pseudomonas, Clostridium, Proteiniphilum, and Bacteroides. The structure of the viral community was significantly affected by pH (P = 0.007, analyzed by RDA) and the bacterial community (R = 0.83, P < 0.001, analyzed by Mantel test). The relative abundance of ARGs showed a strong correlation (R > 0.8, P < 0.01) with viral family, suggesting that viruses play an important role in ARGs dissemination. Phage regulate bacterial population abundance through top-down effects, thus participating in MSW decomposition. These results demonstrate that viral community are involve in ARGs transmission and dissemination and mediate MSW decomposition in landfill.

Exploring the microbial mechanism of reducing methanogenesis during dairy manure membrane-covered aerobic composting at industrial scale

In this study, the microbial mechanism of reducing methanogenesis during membrane-covered aerobic composting from solid dairy manure was investigated. An industrial-scale experiment was carried out to compare a static composting group (SC) and a forced aeration composting group (AC) with a semipermeable membrane-covered composting group (MC + AC). The results showed that the semipermeable membrane-covered could improve the oxygen utilization rate and inhibit the anaerobic bacterial genus Hydrogenispora and archaea order Methanobacteriales. During the membrane-covered period, the acetoclastic methanogenesis module in MC + AC, AC and SC decreased by 0.58%, 0.05% and 0.04%, respectively, and the cdhC gene in the acetoclastic pathway was found to be decreased by 65.51% only in MC + AC. Changes in methane metabolism pathways resulted in a 27.48% lower average methane concentration in MC + AC than in SC. Therefore, the semipermeable membrane-covered strategy can effectively reduce methane production during dairy manure aerobic composting by restricting the methanogenesis of the acetoclastic pathway.

Methanogen Community Dynamics and Methanogenic Function Response to Solid Waste Decomposition

Methane production during solid waste decomposition is a typical methanogen-mediated and enzyme-catalyzed anaerobic digestion (AD). Methanogen community dynamics and metabolic diversity during the decomposition are not known. In this study, we investigated methanogen community dynamics and methanogenic pathways during solid waste decomposition in a bioreactor using high-throughput Illumina MiSeq sequencing and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt), respectively. We also related the methanogen community differences with solid waste and leachate physiochemical parameters. Results showed that the percentage of biodegradable matter (BDM) in solid waste decreased from 55 ± 5% in aerobic phase (AP) to 30 ± 2% in anaerobic acid phase (ACP), and to 13 ± 11% in methanogenic phase (MP), resulting in 76% BDM consumption by microbes. Methanogen community structure varied in AP, ACP, and MP, showing that Methanomicrobiales and Methanosarcinales were dominant in AP and MP and archaea E2 was abundant in ACP. Each phase had abundant core methanogen orders, genera, and species with significant difference (p < 0.05). Redundancy analysis showed that biochemical oxygen demand (BOD₅) and nitrate significantly influenced methanogen community composition, suggesting that methanogen community structure is nutrient-dependent. Two methanogenic pathways including acetoclastic and hydrogenotrophic pathways with associated functional genes differed at three phases. ACP had the lowest abundance of these genes, indicating that methanogenesis was inhibited in acidogenesis. Abundant hydrogenotrophic and acetoclastic methanogenesis functional genes in MP and AP are in response to the abundance of Methanomicrobiales and Methanosarcinales. The findings provide previously unidentified insight into the mechanism of methanogen community structure and function during solid waste bioconversion for methane.