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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. [ABSTRACT FROM AUTHOR]

Little is known regarding how bacterial communities assemble at landfill, as well as how the environment shapes the composition of bacterial community. In this study, up to 42 refuse samples from a large-scale landfill in China were physicochemically and phylogenetically investigated. 16S ribosomal RNA (rRNA) gene-based Illumina MiSeq sequencing (nine samples) revealed that representatives of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Bacteroidetes were dominant in the refuse samples, which was similar to a previous study on landfill leachate by using 454 pyrosequencing. Although 741 operational taxonomic units (OTUs) were detected across all nine samples, 6 of these OTUs were detected in all of the data sets, suggesting difference between bacterial community structures. Geographical differences between the samples, irrespective of depths, were revealed by a principal component analysis (PCA) based on the terminal restriction fragment length polymorphism (TRFLP) profiles of 42 refuse samples. Redundancy analysis (RDA) suggested that environmental heterogeneity (pH, landfilling ages, and depths) and the abundance of bacteria (represented by 16S rRNA gene copy numbers) were the main drivers shaping the bacterial community structure. [ABSTRACT FROM AUTHOR]

Terrestrially derived carbon and nutrients are washed into lakes, providing nutritional drivers for both microbial heterotrophy and phototrophy. Changes in the quantity and diversity of carbon and nutrients exported from watersheds in response to alterations in long-term land use have led to a need for evaluation of the linkage between watershed-exported carbon and nutrients and bacterial community structure in watershed associated lakes. To learn more about these interactions, we investigated Muskrat Lake in Michigan, which has a well-defined moderately sized watershed dominated by agriculture. We measured the water chemistry, characterized the dissolved organic carbon, and determined the structure of the bacterial communities at the inlet and center of this lake (five depths per site) over the summer and fall of 2008. The lake had temporal and rain event-based fluctuations in water chemistry, as well as temporal and rain event-dependent shifts in bacterial communities as measured by terminal restriction fragment length polymorphism. Agricultural watershed inputs were observed in the lake during and after rain events. Terminal restriction fragment length polymorphism and 454 pyrosequencing of the bacterial communities indicated that there were differences over time and that the dominant phylotypes shifted between summer and late fall. Some populations (e.g., Polynucleobacter and Mycobacterium) increased during fall, while others (e.g., Gemmatimonas) diminished. Redundancy and partitioning analyses showed that water chemistry is highly correlated with variations in the bacterial community of the lake, which explained 34 % of the variations in the bacterial community. Dissolved organic carbon had the greatest effects on variations in the Muskrat Lake bacterial community (2 %). The results of this study provide information that will enable a better understanding of the interaction between the bacterial community of lakes and changes in chemical properties as a result of nutrient importation from the surrounding watershed. [ABSTRACT FROM AUTHOR]

Little is known about the archaeal and the bacterial diversities in a landfill during different phases of decomposition. In this study, the archaeal and the bacterial diversities of Laogang landfill (Shanghai, China) at two different decomposition phases (i.e., initial methanogenic phase (IMP) and stable methanogenic phase (SMP)), were culture-independently examined using PCR-based 454 pyrosequencing. A total of 47,753 sequences of 16S rRNA genes were retrieved from 69,954 reads and analyzed to evaluate the diversities of the archaeal and bacterial communities. The most predominant types of archaea were hydrogenotrophic Methanomicrobiales , and of bacteria were Proteobacteria , Firmicutes , and Bacteroidetes. As might be expected, their abundances varied at decomposition phases. Archaea Methanomicrobiales accounts for 97.6% of total archaeal population abundance in IMP and about 57.6% in SMP. The abundance of archaeal genus Halobacteriale was 0.1% in IMP and was 20.3% in the SMP. The abundance of Firmicutes was 21.3% in IMP and was 4.3% in SMP. The abundance of Bacteroidetes represented 11.5% of total bacterial in IMP and was dominant (49.4%) in SMP. Both the IMP and SMP had unique cellulolytic bacteria compositions. IMP consisted of members of Bacillus , Fibrobacter , and Eubacterium , while SMP harbored groups of Microbacterium . Both phases had Clostridium with different abundance, 4–5 folds higher in SMP. [ABSTRACT FROM AUTHOR]

Little is known about the bacterial diversity of landfills and how environmental factors impact the diversity. In this study, PCR-based 454 pyrosequencing was used to investigate the bacterial communities of ten landfill leachate samples from five landfill sites in China. A total of 137 K useable sequences from the V3-V6 regions of the 16S rRNA gene were retrieved from 205 K reads. These sequences revealed the presence of a large number of operational taxonomic units (OTUs) in the landfills (709-1599 OTUs per sample). The most predominant bacterial representatives in the landfills investigated, regardless of geographic area, included Gammaproteobacteria, Firmicutes, and Bacteroidetes. The phyla Fusobacteria and Tenericutes were also found for the first time to be predominant in the landfills. The phylum Fusobacteria predominated (51.5 and 48.8 %) in two semi-arid landfills, and the phylum Tenericutes dominated (30.6 %) at one humid, subtropical landfill. Further, a large number of Pseudomonas was detected in most samples, comprising the dominant group and accounting for 40.9 to 92.4 % of the total abundance. Principal component analysis (PCA) and cluster analysis based on OTU abundance showed that the abundant taxa separated the bacterial community. Canonical correlation analysis (CCA) suggested that precipitation and landfilling age significantly impact on the bacterial community structure. The bacterial community function (e.g., cellulolytic bacteria, sulfate-reducing bacteria (SRB), sulfate-oxidizing bacteria, and xenobiotic organic compound (XOC)-degrading bacteria) was also diverse, but the pattern is unclear. [ABSTRACT FROM AUTHOR]

• Bacterial community diversity significantly differed in refuse decomposition. • Bacterial community structure showed succession pattern. • Proteobacteria , Firmicutes , and Bacteroidetes were the dominant representatives. • MP had higher percentage of carbohydrate metabolism than AP and ACP. • Nitrification and denitrifiation mainly occurred at AP and both AP and MP. Bacterial community structure and metabolic function during solid waste decomposition were investigated using Illumina MiSeq sequencing and phylogenetic investigation of communities by reconstruction of unobserved states, respectively. Results showed that bacterial community diversity and structure differed in aerobic phase, anaerobic acid phase, and methanogenic phase. Anaerobic acid phase had significantly (p < 0.05) higher richness. Proteobacteria , Firmicutes , and Bacteroidetes were the dominant representatives with significant (p < 0.05) difference between three phases. Total nitrogen of solid waste and pH of leachate were the important factors in shaping bacterial community composition. Bacterial metabolism, information storage and processing, and cellular processes and signaling were the primary functions during solid waste decomposition. Key function genes (amo , nar , nis , and nos) profiles suggested that nitrification and denitrifiation mainly occurred in AP and both AP and MP, respectively. [ABSTRACT FROM AUTHOR]

Landfill is important reservoirs of residual antibiotics and antibiotic resistance genes (ARGs), but the mechanism of landfill application influence on antibiotic resistance remains unclear. Although refuse decomposition plays a crucial role in landfill stabilization, its impact on the antibiotic resistance has not been well characterized. To better understand the impact, we studied the dynamics of ARGs and the bacterial community composition during refuse decomposition in a bench-scale bioreactor after long term operation (265 d) based on metagenomics analysis. The total abundances of ARGs increased from 431.0 ppm in the initial aerobic phase (AP) to 643.9 ppm in the later methanogenic phase (MP) during refuse decomposition, suggesting that application of landfill for municipal solid waste (MSW) treatment may elevate the level of ARGs. A shift from drug-specific (bacitracin, tetracycline and sulfonamide) resistance to multidrug resistance was observed during the refuse decomposition and was driven by a shift of potential bacteria hosts. The elevated abundance of Pseudomonas mainly contributed to the increasing abundance of multidrug ARGs ( mexF and mexW ). Accordingly, the percentage of ARGs encoding an efflux pump increased during refuse decomposition, suggesting that potential bacteria hosts developed this mechanism to adapt to the carbon and energy shortage when biodegradable substances were depleted. Overall, our findings indicate that the use of landfill for MSW treatment increased antibiotic resistance, and demonstrate the need for a comprehensive investigation of antibiotic resistance in landfill. [ABSTRACT FROM AUTHOR]

Atmospheric deposition nitrogen (ADN) increases the N content in soil and subsequently impacts microbial activity of soil. However, the effects of ADN on paddy soil microbial activity have not been well characterized. In this study, we studied how red paddy soil microbial activity responses to different contents of ADN through a 10-months ADN simulation on well managed pot experiments. Results showed that all tested contents of ADN fluxes (27, 55, and 82 kg N ha −1 when its ratio of NH 4 + /NO 3 − -N ( R N ) was 2:1) enhanced the soil enzyme activity and microbial biomass carbon and nitrogen and 27 kg N ha −1 ADN had maximum effects while comparing with the fertilizer treatment. Generally, increasing of both ADN flux and R N (1:2, 1:1 and 2:1 with the ADN flux of 55 kg N ha −1 ) had similar reduced effects on microbial activity. Furthermore, both ADN flux and R N significantly reduced soil bacterial alpha diversity ( p < 0.05 ) and altered bacterial community structure (e.g., the relative abundances of genera Dyella and Rhodoblastus affiliated to Proteobacteria increased). Redundancy analysis demonstrated that ADN flux and R N were the main drivers in shaping paddy soil bacteria community. Overall, the results have indicated that increasing ADN flux and ammonium reduced soil microbial activity and changed the soil bacterial community. The finding highlights how paddy soil microbial community response to ADN and provides information for N management in paddy soil. [ABSTRACT FROM AUTHOR]

Real-time CH 4 oxidation in a landfill cover soil was studied using automated gas sampling that determined biogas (CH 4 and CO 2 ) and O 2 concentrations at various depths in a simulated landfill cover soil (SLCS) column reactor. The real-time monitoring system obtained more than 10,000 biogas (CH 4 and CO 2 ) and O 2 data points covering 32 steady states of CH 4 oxidation with 32 different CH 4 fluxes (0.2–125 mol·m −2 ·d −1 ). The kinetics of CH 4 oxidation at different depths (0–20 cm, 20–40 cm, and 40–60 cm) of SLCS were well fit by a CH 4 -O 2 dual-substrate model based on 32 values (averaged, n = 5–15) of equilibrated CH 4 concentrations. The quality of the fit ( R 2 ranged from 0.90 to 0.96) was higher than those reported in previous studies, which suggests that real time monitoring is beneficial for CH 4 oxidation simulations. MiSeq pyrosequencing indicated that CH 4 flux events changed the bacterial community structure (e.g., increased the abundance of Bacteroidetes and Methanotrophs) and resulted in a relative increase in the amount of type I methanotrophs ( Methylobacter and Methylococcales ) and a decrease in the amount of type II methanotrophs ( Methylocystis ). [ABSTRACT FROM AUTHOR]

Anaerobic digestion (AD) is a microbial-mediated biogeochemical process that includes hydrolysis, acidogenesis, acetogenesis and methanogenesis. AD instability usually occurs in the transition from the acidogenesis phase (AP) to the methanogenesis phase (MP) due to over acidification. However, the underlying microbial mechanism of this transition has not been well characterized. In the present study, the transition of bacterial and methanogenic community composition, methanogenesis functional gene expression and metabolic pathways from AP to MP during food waste (FW) AD were investigated in a bioreactor using metagenomics and reverse transcription PCR technology. AP and MP were identified by changes in methane production, gas accumulation, pH and volatile fatty acids (VFAs). Concomitant with the changes in these physiochemical parameters, the bacterial and methanogenic community composition showed succession patterns. The bacterial composition transformed from acidogenic bacteria (Propionispira and Bacteroides) to hydrolytic bacteria (Smithella , Syntrophus and Syntrophorhabdus), and the methanogen composition transformed from the domination of acetoclastic methanogens (Methanosaeta) to the codomination of hydrogenotrophic methanogens (Methanoculleus , Methanolinea and Methanobacterium) and acetoclastic methanogens (Methanosaeta). The expression level of the methanogenesis functional gene mcrA significantly (p < 0.05) increased in response to the increasing methane production. In contrast, acetoclastic methanogenesis as the main methanogenesis metabolic pathway remained stable. These results showed that FWAD key physiochemical parameters drive the variation in microbial community composition and functional genes expression but not the methanogenesis metabolic pathway. The finding suggests that FWAD process may be better predicted by methanogenic functional characteristics than by microbial community composition. • Acetoclastic methanogenesis pathway remained stable in transition. • The bacterial and methanogenic communities showed succession patterns. • Gene mcrA expression levels increased in response of the methane production. • Methanogenic function characteristics are suggested to predict AD process. [ABSTRACT FROM AUTHOR]