Increased methane concentration alters soil prokaryotic community structure along an artificial pH gradient

Landfill intermediate cover soil microbiomes and their potential for mitigating greenhouse gas emissions revealed through metagenomics

Landfills are a major source of anthropogenic methane emissions and have been found to produce nitrous oxide, an even more potent greenhouse gas than methane. Intermediate cover soil (ICS) plays a key role in reducing methane emissions but may also result in nitrous oxide production. To assess the potential for microbial methane oxidation and nitrous oxide production, long sequencing reads were generated from ICS microbiome DNA and reads were functionally annotated for 24 samples across ICS at a large landfill in New York. Further, incubation experiments were performed to assess methane consumption and nitrous oxide production with varying amounts of ammonia supplemented. Methane was readily consumed by microbes in the composite ICS and all incubations with methane produced small amounts of nitrous oxide even when ammonia was not supplemented. Incubations without methane produced significantly less nitrous oxide than those incubated with methane. In incubations with methane added, the observed specific rate of methane consumption was 0.776 +/- 0.055 μg CH4 g dry weight (DW) soil-1 h-1 and the specific rate of nitrous oxide production was 3.64 × 10-5 +/- 1.30 × 10-5 μg N2O g DW soil-1 h-1. The methanotrophs Methylobacter and an unclassified genus within the family Methlyococcaceae were present in the original ICS samples and the incubation samples, and their abundance increased during incubations with methane. Genes encoding particulate methane monooxygenase/ ammonia monooxygenase (pMMO) were much more abundant than genes encoding soluble methane monooxygenase (sMMO) across the landfill ICS. Genes encoding proteins that convert hydroxylamine to nitrous oxide were not highly abundant in the ICS or incubation metagenomes. In total, these results suggest that although ammonia oxidation via methanotrophs may result in low levels of nitrous oxide production, ICS microbial communities have the potential to greatly reduce the overall global warming potential of landfill emissions.

A novel coupled framework for detecting hotspots of methane emission from the vulnerable Indian Sundarban mangrove ecosystem using data-driven models

Coastal mangroves have been lost to deforestation for anthropogenic activities such as agriculture over the past two decades. The genesis of methane (CH₄), a significant greenhouse gas (GHG) with a high potential for global warming, occurs through these mangrove beds. The mangrove forests in the Indian Sundarban deltaic region were studied for pre-monsoonal and post-monsoonal variations of CH₄ emission. Considering the importance of CH₄ emission, a process-based spatiotemporal (PBS) and an analytical neural network (ANN) model were proposed and used to estimate the amount of CH₄ emission from different land use land cover classes (LULC) of mangroves. The field work was performed in 2020, and gas samples of various LULC were directly collected from the mangrove bed using the enclosed box chamber method. Historical climatic data (1960-1989) were used to predict future climate scenarios and associated CH₄ emissions. The analysis and estimation activities were carried out utilizing satellite images from the pre-monsoonal and post-monsoonal seasons of the same year. The study revealed that pre-monsoonal CH₄ emission was higher in the south-west and northern parts of the deforested mangrove of the Indian Sundarban. A sensitivity study of the anticipated models was conducted using a variety of environmental input parameters and related main field observations. The measured precision area under curve of receiver operating characteristics was 0.753 for PBS and 0.718 for ANN models, respectively. The temperature factor (T_f) was the most crucial variable for CH₄ emissions. Based on the PBS model with coupled model intercomparison project-6 temperature data, a global circulation model was run to predict increasing CH₄ emissions up to 2100. The model revealed that the agricultural lands were the prime emitters of CH₄ in the Sundarban mangrove ecosystem.

Response of a methane-driven interaction network to stressor intensification

Microorganisms may reciprocally select for specific interacting partners, forming a network with interdependent relationships. The methanotrophic interaction network, comprising methanotrophs and non-methanotrophs, is thought to modulate methane oxidation and give rise to emergent properties beneficial for the methanotrophs. Therefore, microbial interaction may become relevant for community functioning under stress. However, empirical validation of the role and stressor-induced response of the interaction network remains scarce. Here, we determined the response of a complex methane-driven interaction network to a stepwise increase in NH4Cl-induced stress (0.5-4.75 g L-1, in 0.25-0.5 g L-1 increments) using enrichment of a naturally occurring complex community derived from a paddy soil in laboratory-scale incubations. Although ammonium and intermediates of ammonium oxidation are known to inhibit methane oxidation, methanotrophic activity was unexpectedly detected even in incubations with high ammonium levels, albeit rates were significantly reduced. Sequencing analysis of the 16S rRNA and pmoA genes consistently revealed divergent communities in the reference and stressed incubations. The 16S rRNA-based co-occurrence network analysis revealed that NH4Cl-induced stress intensification resulted in a less complex and modular network, likely driven by less stable interaction. Interestingly, the non-methanotrophs formed the key nodes, and appear to be relevant members of the community. Overall, stressor intensification unravels the interaction network, with adverse consequences for community functioning.

Assessing passive rehabilitation for carbon gains in rain-filled agricultural wetlands

Wetland ecosystems have a disproportionally large influence on the global carbon cycle. They can act as carbon sinks or sources depending upon their location, type, and condition. Rehabilitation of wetlands is gaining popularity as a nature-based approach to helping mitigate climate change; however, few studies have empirically tested the carbon benefits of wetland restoration, especially in freshwater environments. Here we investigated the effects of passive rehabilitation (i.e. fencing and agricultural release) of 16 semi-arid rain-filled freshwater wetlands in southeastern Australia. Eight control sites were compared with older (>10 year) or newer (2-5 year) rehabilitated sites, dominated by graminoids or eucalypts. Carbon stocks (soils and plant biomass), and emissions (carbon dioxide - CO₂; and methane - CH₄) were sampled across three seasons, representing natural filling and drawdown, and soil microbial communities were sampled in spring. We found no significant difference in soil carbon or greenhouse gas emissions between rehabilitated and control sites, however, plant biomass was significantly higher in older rehabilitated sites. Wetland carbon stocks were 19.21 t C_org ha^-1 and 2.84 t C_org ha^-1 for soils (top 20 cm; n = 137) and plant biomass (n = 288), respectively. Hydrology was a strong driver of wetland greenhouse gas emissions. Diffusive fluxes (n = 356) averaged 117.63 mmol CO₂ m² d^-1 and 2.98 mmol CH₄ m² d^-1 when wet, and 124.01 mmol CO₂ m² d^-1 and -0.41 mmol CH₄ m² d^-1 when dry. Soil microbial community richness was nearly 2-fold higher during the wet phase than the dry phase, including relative increases in Nitrososphaerales, Myxococcales and Koribacteraceae and methanogens Methanobacteriales. Vegetation type significantly influenced soil carbon, aboveground carbon, and greenhouse gas emissions. Overall, our results suggest that passive rehabilitation of rain-filled wetlands, while valuable for biodiversity and habitat provisioning, is ineffective for increasing carbon gains within 20 years. Carbon offsetting opportunities may be better in systems with faster sediment accretion. Active rehabilitation methods, particularly that reinstate the natural hydrology of drained wetlands, should also be considered.

Responses of the rhizosphere bacterial community in acidic crop soil to pH: Changes in diversity, composition, interaction, and function

Soil pH is an important predictor of bacterial community composition and diversity. Examining the effects of pH on diversity, structure, interaction, and function of rhizosphere bacterial communities in acidic crop soils provide valuable information for knowing potential role of rhizosphere bacteria in crop yield. Here, we collected soils from artificial greenhouses and applied Illumina Miseq sequencing, quantitative PCR techniques, multiple ecological analysis methods, including topological analysis and functional profiling to analyze our data and validate our hypotheses. We found that the soil physicochemical properties, species diversity, and rhizosphere bacterial community composition were significantly affected by the degree of soil acidification (pH < 5.5 and pH > 5.5) but not vegetation type. Additionally, bacterial absolute abundance increased with higher pH. The 18 soil samples were clustered into two distinct groups of pH < 5.5 and pH > 5.5 at the OTU level, and soil pH had more of an effect on bacterial community composition compared to the other physicochemical variables. In addition, rhizosphere bacteria might presented relatively less competition for survival in pH < 5.5 soils, and bacterial community functions, including nutrient (i.e., carbon, nitrogen, phosphorus, and sulphur) cycling-related enzymes and proteins, were downregulated in more acidic soils (pH < 5.5) based on sequence analysis. To our knowledge, this report is the first to show that pH is a key factor affecting the diversity, structure, interaction, and function of rhizosphere bacterial communities in acidic crop soil in artificial greenhouses. Our findings emphasize that community function and structure of rhizosphere bacteria are closely correlated in more acidic soils, and the decreased crop yield may be correlated with attenuation of the function of the rhizosphere bacterial community.