A culture-based and culture-independent approach to the study of landfill leachate bacterial and archaeal communities

Study on the growth and decline patterns and environmental drivers of pathogens during the stabilization process of simulated landfilling municipal solid waste

Waste and leachate in landfills are substantial reservoirs of pathogens, however information about the risk of pathogen contamination during the stabilization process under different landfill conditions is very limited. In this study, dynamic changes of culturable pathogens, bacteria community, and human bacterial pathogens (HBPs) during the stabilization process under different landfill conditions were investigated, and the environmental drivers were explored. Results showed that total coliforms, Enterococcus, and Staphylococcus aureus were the dominant pathogens detected in waste and leachate samples. During the landfill stabilization process, the concentration of culturable pathogens peaked at the hydrolysis-acidification stage (3.6 × 105 CFU·g-1) in the anaerobic condition, fluctuated from 4.18 × 104 to 5.35 × 105 CFU·g-1 in the anaerobic leachate-recirculation condition, and kept rising (from 4.18 × 104 to 2.12 × 106 CFU·g-1) in the micro-aerobic condition. Moreover, HBPs abundance and diversity in the waste and leachate under micro-aerobic conditions were higher than those under the other two conditions, suggesting a higher risk of pathogen contamination. Sulfate and pH were significantly (p < 0.05) correlated with the composition of bacterial communities and HBPs, likely serving as the major environmental driving factors. Additionally, the interactions between HBPs and functional bacterial groups tended towards cooperative symbiotic relationships, with hydrolytic-acidogenic bacteria promoting the growth and proliferation of most pathogens. These findings will help to understand the changes and environmental drivers of pathogens during landfill stabilization, which will provide a theoretical basis for the risk prevention and control of pathogens in waste disposal.

Optimizing experimental conditions: the role of buffered environments in microbial isolation, physiological studies, and taxonomic characterization

Using a buffered medium is considered essential for enriching and cultivating novel microbial taxa, studying their pH range and optima, and conducting different physiological experiments. Experimental evidence showed that different buffer compounds impact microbial physiology and cell growth differently, and some of them exert toxic and inhibitory effects on organisms under study. Laboratory growth media supplemented with incompatible buffers could also suppress the organism's growth. Therefore, the selection of buffers without the knowledge of their implications on cell growth and physiology in such experiments yields an inaccurate estimate of their physiological abilities and pH range and optima. In this paper, the authors argue against the use of buffered medium to enrich and isolate novel taxa and suggest determining the pH range and optima using unbuffered medium for taxonomic description and physiological characterization. Based on previous literature and our observations, we recommend the use of rich universal laboratory growth medium with their pH adjusted using 1 N NaOH and/or 1 N HCl for such studies, except in cases where the organism cannot grow in such media. However, the pH of the growth medium must be continuously monitored, and in cases where the medium's buffering capacity is compromised, a suitable pH buffer with only a neutral effect on cell growth must be used for more accurate physiological experiments with that organism in the future. Based on the inhibitory effects of buffers on different cells (prokaryotes and eukaryotes) and physiological activities, in this manuscript, we also recommend that the compatibility of the buffers should be first screened before starting any physiological experiments, and any buffer compound should be avoided in the culture medium during the designing of the culturomics protocols for the cultivation of novel taxa from natural samples.

Comparison of Taxonomic Resolutions of Various Typing Methods for Clostridium and Paraclostridium Species Isolated from Landfill Leachate

Anaerobic bacteria and methanogenic archaea at municipal landfill dumping sites play a vital role in the landfill ecology, waste degradation, global warming and climate change. Although landfill works as a cheap way of solid waste management, unmanaged landfill plays a significant role in spreading pollutants and pathogens in natural ecosystems. The genera Clostridium and Paraclostridium are important groups of anaerobic microbes from a public and environmental health perspective. In the present study, we have isolated different species of Clostridium and Paraclostridium from landfill leachate and performed a comparative analysis to understand their role in landfill ecology and public health. Our data indicate that the anoxic zone of landfills acts as a breeding ground for different species of Clostridium and Paraclostridium, including pathogenic species like C. sporogenes and C. argentinense and leachate, plays a crucial role in the spread of Clostridium in soil and water ecosystem and acts as one of the primary sources of a cause of infection in field workers. We also reported that VITEK and MALDI-TOF/MS are not ideal ways to identify Clostridium at the species level, and 16S rRNA gene sequencing should be the method of choice. In the current study, we also demonstrated that members of the genus Clostridium showed better growth response on Brain Heart Infusion (BHI) and Gifu Anaerobic Medium (GAM), and they can be one of the alternatives to existing media for cultivation and physiological studies of Clostridium.

Culture-based and culture-independent approach for the study of the methanogens and obligate anaerobes from different landfill sites

The landfill is a cheap way of solid waste management in developing countries. The majority of landfills are non-sanitary and work as open garbage dumping sites and pose threats to public and environmental health. Therefore, an in-depth understanding of the chemistry and microbiology of landfills is imperative to develop the right policies for landfill management. In the current study, we investigated the chemistry and microbiology of three Indian landfill sites using culture-based and culture-independent molecular approaches. Our data indicate that the nature of landfills varies from site to site in terms of chemistry, pollutants, and pathogens. We also enriched and cultivated three methanogens using an optimized medium and constructed two high-quality draft genomes from enriched microbiomes using metagenome-assembled genome approaches. The phylogenomic study of one draft genome showed the highest 93% sequence similarity with members of Methanomassiliicoccaceae and was always enriched with Acholoplasma and Anaerohalosphaera lusitana. Despite all the efforts, we did not isolate it in pure culture and hypothesized that for the cultivation of some not-yet-cultured methanogen, the presence of other organisms plays an important role, and their syntrophic interaction must be discerned for its successful cultivation in the future. Co-cultivation of amino acid-degrading organisms indicates that their co-culture can assist in boosting the growth of methanogens. In addition, our data indicated that landfill leachate contains a heavy load of pollutants and treatment is a must before discharge in nature or use in irrigation or biofertilizer.

Carbapenemase and extended-spectrum beta-lactamase-producing bacteria in waters originating from a single landfill in Slovenia

Groundwater, rainwater, and leachate associated with a single landfill were analysed to detect extended-spectrum beta-lactamase (ESBL)-producing and carbapenemase (CP)-producing bacteria. After cultivation on three commercial selective-differential media, 240 bacterial isolates were obtained and identified by matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). Isolates from clinically relevant species were further genotyped by enterobacterial repetitive intergenic consensus polymerase chain reaction, and tested for antibiotic susceptibility and presence of CPs and ESBL enzymes. Two ESBL-producing isolates and two isolates producing CPs were detected in rainwater, groundwater, and leachate: Klebsiella oxytoca complex with the gene for the ESBL enzyme CTX-M-1 and the gene for the CP OXA-48, Serratia fonticola with the gene for the ESBL enzyme FONA-2, and Pseudomonas aeruginosa with the gene coding Verona integron-encoded Metallo-beta-lactamases (VIM) metallo-beta-lactamase. Our study indicates that bacteria with ESBL and CP genes can be present in landfill-associated waters.

Pathogens and antibiotic resistance genes during the landfill leachate treatment process: Occurrence, fate, and impact on groundwater

Landfill leachate is an essential source of pathogens and antibiotic resistance genes (ARGs) in the environment. However, information on the removal behavior of pathogens and ARGs during the leachate treatment and the impact on surrounding groundwater is limited. In this study, we investigated the effects of leachate treatment on the removal of pathogens and ARGs with metagenomic sequencing, as well as the impact of landfill effluent on groundwater. It is shown that the leachate treatment could not completely remove pathogens and ARGs. Twenty-nine additional pathogens and twenty-nine ARGs were newly identified in the landfill effluent. The relative abundance of pathogens and multiple antibiotic resistance genes decreased after ultrafiltration but relative abundance increased after reverse osmosis. In addition, the relative abundances of Acinetobacter baumannii, Erwinia amylovora, Escherichia coli, Fusarium graminearum, Klebsiella pneumoniae, and Magnaporthe oryzae, as well as mdtH, VanZ, and blaOXA-53 increased significantly in the landfill effluent compared to the untreated leachate. The relative abundance of some mobile genetic elements (tniA, tniB, tnpA, istA, IS91) in leachate also increased after ultrafiltration and reverse osmosis. The size of pathogens, the size and properties of ARGs and mobile genetic elements, and the materials of ultrafiltration and reverse osmosis membranes may affect the removal effect of pathogens, ARGs and mobile genetic elements in leachate treatment process. Interestingly, the pathogens and ARGs in landfill effluent were transferred to groundwater according to SourceTracker. The ARGs, mobile genetic elements, and pathogens that are difficult to remove in the leachate treatment process, provide a reference for optimizing the leachate treatment process and improving the control of pathogens and ARGs. Furthermore, this study clarifies the effect of landfill leachate sources of pathogens and ARGs in groundwater.