Methane and nitrous oxide cycling microbial communities in soils above septic leach fields: Abundances with depth and correlations with net surface emissions

Greenhouse gas production from an intermittently dosed cold-climate wastewater treatment wetland

This study explores the greenhouse gas (GHG) fluxes of nitrous oxide (N2O), methane (CH4) and carbon dioxide (CO2) from a two-stage, cold-climate vertical-flow treatment wetland (TW) treating ski area wastewater at 3 °C average water temperature. The system is designed like a modified Ludzack-Ettinger process with the first stage a partially saturated, denitrifying TW followed by an unsaturated nitrifying TW and recycle of nitrified effluent. An intermittent wastewater dosing scheme was established for both stages, with alternating carbon-rich wastewater and nitrate-rich recycle to the first stage. The system has demonstrated effective chemical oxygen demand (COD) and total inorganic nitrogen (TIN) removal in high-strength wastewater over seven years of winter operation. Following two closed-loop, intensive GHG winter sampling campaigns at the TW, the magnitude of N2O flux was 2.2 times higher for denitrification than nitrification. CH4 and N2O emissions were strongly correlated with hydraulic loading, whereas CO2 was correlated with surface temperature. GHG fluxes from each stage were related to both microbial activity and off-gassing of dissolved species during wastewater dosing, thus the time of sampling relative to dosing strongly influenced observed fluxes. These results suggest that estimates of GHG fluxes from TWs may be biased if mass transfer and mechanisms of wastewater application are not considered. Emission factors for N2O and CH4 were 0.27 % as kg-N2O-N/kg-TINremoved and 0.04 % kg-CH4-C/kg-CODremoved, respectively. The system had observed seasonal emissions of 600.5 kg CO2 equivalent of GHGs estimated over 130-days of operation. These results indicate a need for wastewater treatment processes to mitigate GHGs.

Greenhouse gas emissions from on-site sanitation systems: A systematic review and meta-analysis of emission rates, formation pathways and influencing factors

Onsite sanitation systems (OSS) are significant sources of greenhouse gases (GHG) including carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O). While a handful of studies have been conducted on GHG emissions from OSS, systematic evaluation of literature on this subject is limited. Our systematic review and meta-analysis provides state-of-the- art information on GHG emissions from OSS and identifies novel areas for investigation. The paper analyzes GHG emission rates from different OSS, the influence of various design, operational, and environmental factors on emission rates and proffers mitigation measures. Following the Preferred Reporting Items for Systematic reviews and Meta-analysis (PRISMA) guidelines, we identified 16 articles which quantified GHG emissions from OSS. Septic tanks emit substantial amounts of CO2 and CH4 ranging from 1.74 to 398.30 g CO2/cap/day and 0.06-110.13 g CH4/cap/day, respectively, but have low N2O emissions (0.01-0.06 g N₂O/cap/day). CH4 emissions from pit latrines range from 0.77 to 20.30 g CH4/cap/day N2O emissions range from 0.76 to 1.20 gN2O/cap/day. We observed statistically significant correlations (p < 0.05) between temperature, biochemical oxygen demand, chemical oxygen demand, dissolved oxygen, storage period, and GHG emissions from OSS. However, no significant correlation (p > 0.05) was observed between soil volumetric water content and CO2 emissions. CH4 emissions (expressed as CO2 equivalents) from OSS estimated following Intergovernmental Panel for Climate Change (IPCC) guidelines were found to be seven times lower (90.99 g CO2e/cap/day) than in-situ field emission measurements (704.7 g CO2e/cap/day), implying that relying solely on IPCC guidelines may lead to underestimation of GHG emission from OSS. Our findings underscore the importance of considering local contexts and environmental factors when estimating GHG emissions from OSS. Plausible mitigation measures for GHG emissions from OSS include converting waste to biogas in anaerobic systems (e.g. biogas), applying biochar, and implementing mitigation policies that equally address inequalities in sanitation service access. Future research on GHG from OSS should focus on in-situ measurements of GHGs from pit latrines and other common OSS in developing countries, understanding the fate and transport of dissolved organics like CH4 in OSS effluents and impacts of microbial communities in OSS on GHG emissions. Addressing these gaps will enable more holistic and effective management of GHG emissions from OSS.

Sediment prokaryotic microbial community and potential biogeochemical cycle from saline lakes shaped by habitat

The microbial diversity and ecological function in different saline lakes was reduced or disappeared as the influence of climate change and human activities even before they were known. However, reports about prokaryotic microbial of saline lakes from Xinjiang are very limited especially in large-scale investigations. In this study, a total of 6 saline lakes represented three different habitats, including hypersaline lake (HSL), arid saline lake (ASL), and light saltwater lake (LSL) were involved. The distribution pattern and potential functions of prokaryotes were investigated by using the cultivation-independent method of amplicon sequencing. The results showed that Proteobacteria was the predominant community and was widely distributed in all kinds of saline lakes, Desulfobacterota was the representative community in hypersaline lakes, Firmicutes and Acidobacteriota were mainly distributed in arid saline lake samples, and Chloroflexi was more abundant in light saltwater lakes. Specifically, the archaeal community was mainly distributed in the HSL and ASL samples, whereas it was very rare in the LSL lakes. The functional group showed that fermentation was the main metabolic process of microbes in all saline lakes and covered 8 phyla, including Actinobacteriota, Bacteroidota, Desulfobacterota, Firmicutes, Halanaerobiaeota, Proteobacteria, Spirochaetota, and Verrucomicrobiota. Among the 15 functional phyla, Proteobacteria was a distinctly important community in saline lakes, as it exhibited wide functions in the biogeochemical cycle. According to the correlation of environmental factors, SO₄^2-, Na⁺, CO₃^2-, and TN were significantly affected in the microbial community from saline lakes in this study. Overall, our study provided more detailed information about microbial community composition and distribution from three different habitats of saline lakes, especially the potential functions of carbon, nitrogen, and sulfur cycles, which provided new insight for understanding the complex microbiota adapt to the extreme environment and new perspectives on evaluating microbial contributions to degraded saline lakes under environmental change.

Linking Transcriptional Dynamics of Peat Microbiomes to Methane Fluxes during a Summer Drought in Two Rewetted Fens

Rewetted peatlands are reestablished hot spots for CH₄ emissions, which are subject to increased drought events in the course of climate change. However, the dynamics of soil methane-cycling microbiomes in rewetted peatlands during summer drought are still poorly characterized. Using a quantitative metatranscriptomic approach, we investigated the changes in the transcript abundances of methanogen and methanotroph rRNA, as well as mcrA and pmoA mRNA before, during, and after the 2018 summer drought in a coastal and a percolation fen in northern Germany. Drought changed the community structure of methane-cycling microbiomes and decreased the CH₄ fluxes as well as the rRNA and mRNA transcript abundances of methanogens and methanotrophs, but they showed no recovery or increase after the drought ended. The rRNA transcript abundance of methanogens was not correlated with CH₄ fluxes in both fens. In the percolation fen, however, the mcrA transcript abundance showed a positive and significant correlation with CH₄ fluxes. Importantly, when integrating pmoA abundance, a stronger correlation was observed between CH₄ fluxes and mcrA/pmoA, suggesting that relationships between methanogens and methanotrophs are the key determinant of CH₄ turnover. Our study provides a comprehensive understanding of the methane-cycling microbiome feedbacks to drought events in rewetted peatlands.

Effects of organic fertilization on functional microbial communities associated with greenhouse gas emissions in paddy soils

Soil microbial communities play a key role in the biochemical processes and nutrient cycles of the soil ecosystem and their byproducts, including greenhouse gases (GHGs). Organic fertilization influences bacterial soil biodiversity and is an essential emission source of GHGs in paddy soil ecosystems. However, the impact of organic fertilization on the functional microorganisms associated with the GHGs methane and nitrous oxide remains unknown. We conducted paddy soil field experiments under three different treatments (no fertilization, base fertilization, and organic fertilization) to investigate the contribution of organic fertilization to soil nutrients and the functional microorganisms associated with GHG emissions. We found that organic fertilization effectively increased the soil organic matter (P < 0.001), soil organic carbon (P < 0.001), and total nitrogen (P < 0.05) as well as the richness (operational taxonomic units and abundance-based coverage estimators) of the methanogenic communities. Correlation analyses showed that methanogenic communities that were present in abundance were more vulnerable to perturbations in soil properties compared to nitrifying bacterial communities. Partial least squares path model analyses elucidated that organic fertilization directly affected both methanogenic communities and nitrifying bacterial communities (P < 0.05), thereby accelerating methane emissions. Strong co-occurrence networks were observed within the soil-dominant phyla Acidobacteria, Bacteroidetes, and Proteobacteria. Our findings highlight the impact of organic fertilization on soil nutrients and functional microorganisms and guide mitigating GHG emissions from paddy soil agroecosystems.

Insights into the microbial community of treated wastewater, its year-round variability and impact on the receiver, using cultivation, microscopy and amplicon-based methods

Apart from chemical constituents, wastewater treatment plant (WWTP) effluents also release microorganisms that can be important to the receiving water bodies either from a sanitary point of view, or taking to the account the biogeochemical potential of the recipients. However, little is known about the treated wastewater microbial community, its composition, seasonal changes, functions and fate in the waters of the receiver. Thus, this study presents a synergistic approach coupling new and traditional methods: analytical chemistry, classical microbiology (cultivation- and microscopy-based methods), as well as Next Generation Sequencing and a quantitative real-time polymerase chain reaction (qPCR). The results show that in terms of bacterial community composition, treated wastewater differed from the environmental samples, irrespectively if they were related or unrelated to the WWTP effluent discharge. The canonical correspondence analysis (CCA) taking into account chemical parameters and taxonomical biodiversity indirectly confirmed the seasonal deterioration of the treated wastewater quality as a result of temperature-driven change of activated sludge community structure and biomass washout (observed also by DAPI staining). Despite seasonal fluctuations of total suspended solids and inter-related parameters (such as COD, BOD, TN, TP), the treated wastewater quality remained within current discharge limits. It was due to treatment processes intensively adjusted by WWTP operators, particularly those necessary to maintain an appropriate rate of autotrophic processes of nitrification and to support biological phosphorus removal. This can explain the observed microbiome composition similarity among WWTP effluents at high taxonomic levels. Obtained data also suggest that besides wastewater treatment efficiency, WWTP effluents are still sources of both human-related microorganisms as well as bacteria equipped in genes involved in N-cycling. Their potential of participation in nutrients cycling in the receivers is widely unknown and require critical attention and better understanding.

Changes in Soil Chemical Properties Due to Long-Term Compost Fertilization Regulate Methane Turnover Related Gene Abundances in Rice Paddy

Maintaining rice yield, soil function, and fertility are essential components of long-term compost fertilization. However, paddy fields are major sources of anthropogenic methane emissions. The aim of the study is to evaluate the changes in soil chemical properties and their concurrent impact on the abundance of methanogenesis (mcrA) and methane oxidation (pmoA) related genes among compost (Com), NPK+Compost (NPKCom), and unfertilized (NF) fallow paddy fields under long-term compost fertilization. Results showed that compost and NPK+Compost fertilization altered the soil chemical properties of paddy fields with a significant increase in the functional gene abundance potentially associated with Methanobacteriaceae for mcrA (1.23 × 106 to 3.84 × 106 copy number g−1 dry soil) and methane oxidizing bacteria such as Methylomonas and Methylobacter for pmoA (1.65 × 106 to 4.3 × 106 copy number g−1 dry soil). Ordination plots visualized these changes, where treatments clustered distinctly indicating that Com and NPKCom treatments were characterized by paddy soils with elevated OM, TN, K and P content and higher abundances of methanogenesis and methane oxidation related genes. The study showed that long-term compost fertilization resulted in paddy fields with high nutrient content and high gene abundance, attributed to methanogens and methane oxidizing bacteria that responded well with compost fertilization. These results indicated the potential of these fallow paddy fields for methane emission and methane oxidation and that they are ‘primed’, potentially influencing subsequent paddy field responses to long-term compost application.

Methane Monooxygenase Gene Transcripts as Quantitative Biomarkers of Methanotrophic Activity in Methylosinus trichosporium OB3b

Methanotrophic microorganisms are characterized by their ability to oxidize methane. Globally they have a significant impact on methane emissions by attenuating net methane fluxes to the atmosphere in natural and engineered systems, though the populations are dynamic in their activity level in soils and waters. Methanotrophs oxidize methane using methane monooxygenase (MMO) enzymes, and selected subunit genes of the most common MMOs, specifically pmoA and mmoX, are used as biomarkers for the presence and abundance of populations of bacterial methanotrophs. The relative expression of these biomarker genes is dependent on copper-to-biomass ratios. Empirically derived quantitative relationships between methane oxidation biomarker transcript amounts and methanotrophic activity could facilitate determination of methane oxidation rates. In this study, pure cultures of a model type II methanotroph, Methylosinus trichosporium OB3b, were grown in hollow-fiber membrane bioreactors (HFMBR) under different steady-state methane oxidation conditions. Methanotroph biomass (DNA based) and methane oxidation biomarker mRNA transcript amounts were determined using quantitative PCR (qPCR) and reverse transcription-PCR (RT-qPCR), respectively. Under both copper-present and copper-limited conditions, per-cell pmoA mRNA transcript levels positively correlated with measured per-cell methane oxidation rates across 3 orders of magnitude. These correlations, if maintained across different methanotrophs, could prove valuable for inferring in situ oxidation rates of methanotrophs and understanding the dynamics of their impact on net methane emissions.IMPORTANCE Methanotrophs are naturally occurring microorganisms capable of oxidizing methane and have an impact on global net methane emissions. The genes pmoA and mmoX are used as biomarkers for bacterial methanotrophs. Quantitative relationships between transcript amounts of these genes and methane oxidation rates could facilitate estimation of methanotrophic activity. In this study, a strong correlation was observed between per-cell pmoA transcript levels and per-cell methane oxidation rates for pure cultures of the aerobic methanotroph M. trichosporium OB3b grown in bioreactors. If similar relationships exist across different methanotrophs, they could prove valuable for inferring in situ oxidation rates of methanotrophs and better understanding their impact on net methane emissions.

Structure of greenhouse gas-consuming microbial communities in surface soils of a nitrogen-removing experimental drainfield

Septic systems represent a source of greenhouse gases generated by microbial processes as wastewater constituents are degraded. Both aerobic and anerobic wastewater transformation processes can generate nitrous oxide and methane, both of which are potent greenhouse gases (GHGs). To understand how microbial communities in the surface soils above shallow drainfields contribute to methane and nitrous oxide consumption, we measured greenhouse gas surface flux and below-ground concentrations and compared them to the microbial communities present using functional genes pmoA and nosZ. These genes encode portions of particulate methane monooxygenase and nitrous oxide reductase, respectively, serving as a potential sink for the respective greenhouse gases. We assessed the surface soils above three drainfields served by a single household: an experimental layered passive N-reducing drainfield, a control conventional drainfield, and a reserve drainfield not in use but otherwise identical to the control. We found that neither GHG flux, below-ground concentration or soil properties varied among drainfield types, nor did methane oxidizing and nitrous oxide reducing communities vary by drainfield type. We found differences in pmoA and nosZ communities based on depth from the soil surface, and differences in nosZ communities based on whether the sample came from the rhizosphere or surrounding bulk soils. Type I methanotrophs (Gammaproteobacteria) were more abundant in the upper and middle portions of the soil above the drainfield. In general, we found no relationship in community composition for either gene based on GHG flux or below-ground concentration or soil properties (bulk density, organic matter, above-ground biomass). This is the first study to assess these communities in the surface soils above an experimental working drainfield, and more research is needed to understand the dynamics of greenhouse gas production and consumption in these systems.

Nitrifying and Denitrifying Microbial Communities in Centralized and Decentralized Biological Nitrogen Removing Wastewater Treatment Systems

Biological nitrogen removal (BNR) in centralized and decentralized wastewater treatment systems is assumed to be driven by the same microbial processes and to have communities with a similar composition and structure. There is, however, little information to support these assumptions, which may impact the effectiveness of decentralized systems. We used high-throughput sequencing to compare the structure and composition of the nitrifying and denitrifying bacterial communities of nine onsite wastewater treatment systems (OWTS) and one wastewater treatment plant (WTP) by targeting the genes coding for ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ). The amoA diversity was similar between the WTP and OWTS, but nosZ diversity was generally higher for the WTP. Beta diversity analyses showed the WTP and OWTS promoted distinct amoA and nosZ communities, although there is a core group of N-transforming bacteria common across scales of BNR treatment. Our results suggest that advanced N-removal OWTS have microbial communities that are sufficiently distinct from those of WTP with BNR, which may warrant different management approaches.

Spatial and temporal variation of CO2 and CH4 emissions from a septic tank soakaway

CO₂ and CH₄ flux measurements over a septic tank soakaway located in a northern maritime climate (Ireland) were conducted for a period of 81 days using a multi-chamber automated soil gas flux chamber system with high spatial and temporal resolution. Overall median CO₂ fluxes were 7.28; 6.40 μmol CO₂ m^-2 s^-1 from the soakaway and control soil, respectively. Overall median CH₄ fluxes were - 0.28; -0.67 nmol CH₄ m^-2 s^-1 from the soakaway and control soil, respectively. While CO₂ fluxes expressed strong diurnal variability driven by soil temperature, CH₄ fluxes were less affected by environmental factors and effectively limited to the first few meters from the septic tank. However, localised CH₄ degassing events were observed during drying conditions with up to 60-times higher fluxes compared to the overall median. The soakaway was found to be a net emitter of both CO₂ and CH₄, releasing a total of 7.327 kg CO₂ yr^-1 and 0.033 kg CO_2Eq. yr^-1, respectively. The apparent spatio-temporal heterogeneity of observed soil gas fluxes identified in this study emphasises the importance of integrating measurements with both high spatial and temporal resolution from on-site installations as engineered nature-based solutions.

Microbial communities controlling methane and nutrient cycling in leach field soils

Septic systems inherently rely on microbial communities in the septic tank and leach field to attenuate pollution from household sewage. Operating conditions of septic leach field systems, especially the degree of water saturation, are likely to impact microbial biogeochemical cycling, including carbon (C), nitrogen (N), and phosphorus (P), as well as greenhouse gas (GHG) emissions to the atmosphere. To study the impact of flooding on microbial methane (CH₄) and nutrient cycling, two leach field soil columns were constructed. One system was operated as designed and the other was operated in both flooded and well-maintained conditions. CH₄ emissions were significantly higher in flooded soils (with means between 0.047 and 0.33 g CH₄ m^-2 d^-1) as compared to well-drained soils (means between -0.0025 and 0.004 g CH₄ m^-2 d^-1). Subsurface CH₄ profiles were also elevated under flooded conditions and peaked near the wastewater inlet. Gene abundances of mcrA, a biomarker for methanogens, were also greatest near the wastewater inlet. In contrast, gene abundances of pmoA, a biomarker for methanotrophs, were greatest in surface soils at the interface of CH₄ produced subsurface and atmospheric oxygen. 16S rRNA, mcrA, and pmoA amplicon library sequencing revealed microbial community structure in the soil columns differed from that of the original soils and was driven largely by CH₄ fluxes and soil VWC. Additionally, active microbial populations differed from those present at the gene level. Flooding did not appear to affect N or P removals in the soil columns (between 75 and 99% removal). COD removal was variable throughout the experiment, and was negatively impacted by flooding. Our study shows septic system leach field soils are dynamic environments where CH₄ and nutrients are actively cycled by microbial populations. Our results suggest proper siting, installation, and routine maintenance of leach field systems is key to reducing the overall impact of these systems on water and air quality.