Increased fermentation activity and persistent methanogenesis in a model aquifer system following source removal of an ethanol blend release

Mechanism of microbial regulation on methane metabolism in saline-alkali soils based on metagenomics analysis

Saline-alkali soils constitute a globally important carbon pool that plays a critical role in soil carbon dioxide (CO2) and methane (CH4) fluxes. However, the relative importance of microorganisms in the regulation of CH4 emissions under elevated salinity remains unclear. Here, we report the composition of CH4 production and oxidation microbial communities under five different salinity levels in the Yellow River Delta, China. This study also obtained the gene number of microbial CH4 metabolism via testing the soil metagenomes, and further investigated the key soil factors to determine the regulation mechanism. Spearman correlation analysis showed that the soil electrical conductivity, salt content, and Na+, and SO42- concentrations showed significantly negative correlations with the CO2 and CH4 emission rates, while the NO2--N concentration and NO2-/NO3- ratio showed significantly positive correlations with the CO2 and CH4 emission rates. Metabolic pathway analysis showed that the mcrA gene for CH4 production was highest in low-salinity soils. By contrast, the relative abundances of the fwdA, ftr, mch, and mer genes related to the CO2 pathway increased significantly with rising salinity. Regarding CH4 oxidation processes, the relative abundances of the pmoA, mmoB, and mdh1 genes transferred from CH4 to formaldehyde decreased significantly from the control to the extreme-salinity plot. The greater abundance and rapid increase of methanotrophic bacteria compared with the lower abundance and slow increase in methanogenic archaea communities in saline-alkali soils may have increased CH4 oxidation and reduced CH4 production in this study. Only CO2 emissions positively affected CH4 emissions from low- to medium-salinity soils, while the diversities of CH4 production and oxidation jointly influenced CH4 emissions from medium- to extreme-salinity plots. Hence, future investigations will also explore more metabolic pathways for CH4 emissions from different types of saline-alkali lands and combine the key soil enzymes and regulated biotic or abiotic factors to enrich the CH4 metabolism pathway in saline-alkali soils.

Anaerobic mineralization of toluene by enriched soil-free consortia with solid-phase humin as a terminal electron acceptor

The anaerobic biodegradation of toluene proceeds very slowly owing to limited electron acceptors in contaminated aquifer. The liquid reagents traditionally used to enhance this process readily migrate away from the contaminated site, and continuous addition would cause secondary pollution. In our previous study, the reduced solid-phase humic substances (humin), which are redox active, were found to act as electron donors to promote the microbial reactions. Here, we provide new evidence that humin can promote the anaerobic biodegradation of toluene as a terminal electron acceptor. When inoculating nitrate-reducing (NR) and iron-reducing (IR) consortia with toluene degradation activities, the average toluene degradation rates reached 21.20 ± 1.18 μmol/(L·d) and 15.43 ± 0.41 μmol/(L·d) in the presence of a sediment humin (HMcj), and 94.69% ± 4.26% and 93.20% ± 3.73% of the electrons released from toluene oxidation to CO₂ could be recovered by the reduction of HMcj, respectively. Spectroscopy analyses revealed that quinone moieties and nitrogen-containing moieties may be the electron-accepting groups of HMcj. Based on 16S rRNA sequencing, Cellulomonas spp. were the possible functional bacteria in the culture with NR consortium as the inoculum, while Azospira spp., Cellulomonas spp. and Bacillus spp. were the possible functional bacteria in the culture with IR consortium as the inoculum. Further Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analyses indicated that toluene oxidation and extracellular electron transfer functions were more abundant in HMcj amended cultures, suggesting a possible enhancement mechanism by HMcj. Additionally, experiments using natural groundwater illustrated that toluene degradation was highly dependent on its concentration, HMcj dosage, pH, and salinity. The study of a column filled with HMcj-coated quartz sand demonstrated a desirable level of toluene degradation in a continuous-flow mode without the presence of other electron acceptors. This study provided an effective and green approach for the remediation of the toluene-contaminated groundwater.

Natural Source Zone Depletion (NSZD) Quantification Techniques: Innovations and Future Directions

Natural source zone depletion (NSZD) is an emerging technique for sustainable and cost-effective bioremediation of light non-aqueous phase liquid (LNAPL) in oil spill sites. Depending on regulatory objectives, NSZD has the potential to be used as either the primary or sole LNAPL management technique. To achieve this goal, NSZD rate (i.e., rate of bulk LNAPL mass depletion) should be quantified accurately and precisely. NSZD has certain characteristic features that have been used as surrogates to quantify the NSZD rates. This review highlights the most recent trends in technology development for NSZD data collection and rate estimation, with a focus on the operational and technical advantages and limitations of the associated techniques. So far, four principal techniques are developed, including concentration gradient (CG), dynamic closed chamber (DCC), CO2 trap and thermal monitoring. Discussions revolving around two techniques, “CO2 trap” and “thermal monitoring”, are expanded due to the particular attention to them in the current industry. The gaps of knowledge relevant to the NSZD monitoring techniques are identified and the issues which merit further research are outlined. It is hoped that this review can provide researchers and practitioners with sufficient information to opt the best practice for the research and application of NSZD for the management of LNAPL impacted sites.

The process of methanogenesis in paddy fields under different elevated CO2 concentrations

Understanding the process of methanogenesis in paddy fields under the scenarios of future climate change is of great significance for reducing greenhouse gas emissions and regulating the soil carbon cycle. Methyl Coenzyme M Reductase subunit A (mcrA) of methanogens is a rate-limiting enzyme that catalyzes the final step of CH₄ production. However, the mechanism of methanogenesis change in the paddy fields under different elevated CO₂ concentrations (e[CO₂]) is rarely explored in earlier studies. In this research, we explored how the methanogens affect CH₄ flux in paddy fields under various (e[CO₂]). CH₄ flux and CH₄ production potential (MPP), and mcrA gene abundance were quantitatively analyzed under C (ambient CO₂ concentration), C₁ (C + 160 ppm CO₂), and C₂ (C + 200 ppm CO₂) treatments. Additionally, the community composition and structure of methanogens were also compared with Illumina MiSeq sequencing. The results showed that C₂ treatment significantly increased CH₄ flux and MPP at the tillering stage. E[CO₂] had a positive effect on the abundance of methanogens, but the effect was insignificant. We detected four known dominant orders of methanogenesis in this study, such as Methanosarcinales, Methanobacteriales, Methanocellales, and Methanomicrobiales. Although e[CO₂] did not significantly change the overall community structure and diversity of methanogens, C₂ treatment significantly reduced the relative abundance of two uncultured genera compared to C treatment. A linear regression model of DOC, methanogenic abundance, and MPP can explain 67.2% of the variation of CH₄ flux under e[CO₂]. Overall, our results demonstrated that CH₄ flux in paddy fields under e[CO₂] was mainly controlled by soil unstable C substrate and the abundance and activity of methanogens in rhizosphere soil.

Effects of different fertilizers on methane emissions and methanogenic community structures in paddy rhizosphere soil

Paddy soil accounts for 10% of global atmospheric methane (CH₄) emissions. Many types of fertilizers may enhance CH₄ emissions, especially organic fertilizer. The aim of this study was to explore the effects of different fertilizers on CH₄ and methanogen patterns in paddy soil. This experiment involved four treatments: chemical fertilizer (CT), organic fertilizer (OT), mixed with chemical and organic fertilizer (MT), and no fertilizer (ctrl). The three fertilization treatments were applied with total nitrogen at the same rate of 300 kg N ha^-1. Paddy CH₄, soil physicochemical variables and methanogen communities were quantitatively analyzed. Rhizosphere soil mcrA and pmoA gene copy numbers were determined by qPCR. Methanogenic 16S rRNA genes were identified by MiSeq sequencing. The results indicated CH₄ emissions were significantly higher in OT (145.31 kg ha^-1) than MT (84.62 kg ha^-1), CT (77.88 kg ha^-1) or ctrl (32.19 kg ha^-1). Soil organic acids were also increased by organic fertilization. CH₄ effluxes were significantly and negatively related to mcrA and pmoA gene copy numbers, and positively related to mcrA/pmoA. Above all, hydrogenotrophic Methanocella and acetoclastic Methanosaeta were the predominant methanogenic communities; these communities were strictly associated with soil potassium, oxalate, acetate, and succinate. Application of organic fertilizer promoted the dominant acetoclastic methanogens, but suppressed the dominant hydrogenotrophic methanogens. The transformation in methanogenic community structure and enhanced availability of C substrates may explain the increased CH₄ production in OT compared to other treatments. Compared to OT, MT may partially mitigate CH₄ emissions while guaranteeing a high rice yield. On this basis, we recommend the local fertilization pattern should change from 300 N kg ha^-1 of organic manure to the same level of mixed fertilization. Moreover, we suggest multiple combinations of mixed fertilization merit more investigation in the future.

Groundwater ecosystem resilience to organic contaminations: microbial and geochemical dynamics throughout the 5-year life cycle of a surrogate ethanol blend fuel plume

The capacity of groundwater ecosystem to recover from contamination by organic chemicals is a vital concern for environmental scientists. A pilot-scale aquifer system was used to investigate the long-term dynamics of contaminants, groundwater geochemistry, and microbial community structure (by 16S rRNA gene pyrosequencing and quantitative real-time PCR) throughout the 5-year life cycle of a surrogate ethanol blend fuel plume (10% ethanol + 50 mg/L benzene + 50 mg/L toluene). Two-year continuous ethanol-blended release significantly changed the groundwater geochemistry (resulted in anaerobic, low pH, and organotrophic conditions) and increased bacterial and archaeal populations by 82- and 314-fold respectively. Various anaerobic heterotrophs (fermenters, acetogens, methanogens, and hydrocarbon degraders) were enriched. Two years after the release was shut off, all contaminants and their degradation byproducts disappeared and groundwater geochemistry completely restored to the pre-release states (aerobic, neutral pH, and oligotrophic). Bacterial and archaeal populations declined by 18- and 45-fold respectively (relative to the time of shut off). Microbial community structure reverted towards the pre-release states and alpha diversity indices rebounded, suggesting the resilience of microbial community to ethanol blend releases. We also found shifts from O2-sensitive methanogens (e.g., Methanobacterium) to methanogens that are not so sensitive to O2 (e.g., Methanosarcina and Methanocella), which is likely to contribute to the persistence of methanogens and methane generation following the source removal. Overall, the rapid disappearance of contaminants and their metabolites, rebound of geochemical footprints, and resilience of microbial community unequivocally document the natural capacity of groundwater ecosystem to attenuate and recover from a large volume of catastrophic spill of ethanol-based biofuel.

Succession of microbial functional communities in response to a pilot-scale ethanol-blended fuel release throughout the plume life cycle

GeoChip, a comprehensive gene microarray, was used to examine changes in microbial functional gene structure throughout the 4-year life cycle of a pilot-scale ethanol blend plume, including 2-year continuous released followed by plume disappearance after source removal. Canonical correlation analysis (CCA) and Mantel tests showed that dissolved O2 (which was depleted within 5 days of initiating the release and rebounded 194 days after source removal) was the most influential environmental factor on community structure. Initially, the abundance of anaerobic BTEX degradation genes increased significantly while that of aerobic BTEX degradation genes decreased. Gene abundance for N fixation, nitrification, P utilization, sulfate reduction and S oxidation also increased, potentially changing associated biogeochemical cycle dynamics. After plume disappearance, most genes returned to pre-release abundance levels, but the final functional structure significantly differed from pre-release conditions. Overall, observed successions of functional structure reflected adaptive responses that were conducive to biodegradation of ethanol-blend releases.