The Long-Term Relationship between Microbial Metabolism and Greenhouse Gases

Clay-hydrochar composites mitigated CH4 and N2O emissions from paddy soil: A whole rice growth period investigation

With the favorable microporous structure and excellent adsorption capacity, clay-hydrochar composites (CHCs) serve as promising materials to mitigate greenhouse gas emissions (GHG) from the paddy fields. Three clays were co-pyrolyzed with hydrochar derived from poplar sawdust to obtain CHCs, which were applied to the paddy fields to investigate the effects on methane (CH₄) and nitrous oxide (N₂O) emissions. Three CHCs were labeled as bentonite-hydrochar composite (BTHC), montmorillonite-hydrochar composite (MTHC), and kaolinite-hydrochar composite (KTHC), respectively. The effects of these three CHCs on GHG emissions were determined by monitoring the dynamic CH₄ and N₂O emissions in the paddy soil column ecosystem during the rice-growing season. The results showed that compared with the control group, three CHCs significantly mitigated CH₄ and N₂O emissions by 21.4%-47.5% and 5.2%-36.8%, respectively. Furthermore, the fluorescent components result displayed CHCs increased humic-like content by 29.62%-59.72%. A structural equation model was used to assess the hypothesis mitigation mechanism, which exemplified that GHG emissions negatively correlated with pmoA and nosZ genes, possibly resulting in the CH₄ and N₂O mitigation. Among the three CHCs, the KTHC amendment mitigated the CH₄ and N₂O emissions by 47.5% and 36.8%, respectively, which was superior to BTHC and MTHC. Hence, it was recommended for application to the field. Overall, this study demonstrates the mitigating effects of CHCs on GHG emissions for the first time, and the reduced CH₄ and N₂O emissions could contribute to increased soil C and N retention for better agricultural nutrients management.

Haloalkaliphilic denitrifiers-dependent sulfate-reducing bacteria thrive in nitrate-enriched environments

As bridge in global cycles of carbon, nitrogen, and sulfur, sulfate-reducing bacteria (SRB) play more and more important role under various environments, especially the saline-alkali environments with significant increase in area caused by human activities. Sulfate reduction can be inhibited by environmental nitrate. However, how SRB cope with environmental nitrate stress in these extreme environments still remain unclear. Here, after a long-term enrichment of sediment from saline-alkali Qinghai Lake of China using anaerobic filter reactors, nitrate was added to evaluate the response of SRB. With the increase in nitrate concentrations, the inhibition on sulfate reduction was gradually observed. Interestingly, extension of hydraulic retention time can relieve the inhibition caused by high nitrate concentration. Mass balance analysis showed that nitrate reduction is prior to sulfate reduction. Further metatranscriptomic analysis shows that, genes of nitrite reductase (periplasmic cytochrome c nitrite reductase gene) and energy metabolisms (lactate dehydrogenase, formate dehydrogenase, pyruvate:ferredoxin-oxidoreductase, and fumarate reductase genes) in SRB was down-regulated, challenging the long-held opinion that up-regulation of these genes can relieve the nitrate inhibition. Most importantly, the nitrate addition activated the denitrification pathway in denitrifying bacteria (DB) via significantly up-regulating the expression of the corresponding genes (nitrite reductase, nitric oxide reductase c subunit, nitric oxide reductase activation protein and nitrous oxide reductase genes), quickly reducing the environmental nitrate and relieving the nitrate inhibition on SRB. Our findings unravel that in response to environmental nitrate stress, haloalkaliphilic SRB show dependency on DB, and expand our knowledge of microbial relationship during sulfur and nitrogen cycles.

Divergent effects of hydrological alteration and nutrient addition on greenhouse gas emissions in the water level fluctuation zone of the Three Gorges Reservoir, China

Changes in global rainfall patterns and construction of artificial dams have led to widespread alteration of hydrological processes in riparian ecosystems. At the same time, many riparian ecosystems, such as those associated with the Yangtze, are being subjected to enhanced inputs of nitrogen (N) and phosphorus (P) due to intensified agricultural activity in surrounding uplands. Together, these environmental changes may alter the magnitude and direction of greenhouse gasses (GHGs) fluxes from riparian soils. We conducted an in situ experiment combined with quantitative PCR approach (qPCR) to elucidate the effects of hydrological alterations (continuous flooding (CF), periodic flooding (PF), and no flooding (NF)) and nutrient addition (N addition (urea, 100 kg N ha^-1 y^-1), P addition (P₂O₅, 20 kg ha^-1y^-1), N + P addition, and control (CK)) on three major GHGs including carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O) fluxes as well as the underlying mechanisms. Our results showed that hydrological alterations greatly affected GHGs emissions, possibly by altering soil moisture, soil organic C, and C:N ratios. The CF, with higher soil moisture and lower C:N ratio, increased CH₄ emissions 13-fold and reduced CO₂ and N₂O emissions by 37.3% and 72.2% averaged over the growing seasons compared with no flooding. PF enhanced CH₄ emissions 5.7-fold and decreased N₂O emissions by 69.0% in comparison with no flooding. Nutrient additions had no significant effect on CO₂ or CH₄ flux, but P addition significantly lowered N₂O flux. Interactions between hydrological alterations and nutrient additions were not detected for any GHGs. As a result, hydrological alterations and nutrient additions affected the global warming potential (GWP) of growing season GHG budgets on a 100-year time horizon, mainly by changing the CO₂ emissions. CF reduced GWP from 597 to 439 g CO₂-eq m^-2, and N + P addition enhanced GWP from 489 to 625 g CO₂-eq m^-2. The qPCR analysis revealed that decreased CH₄ oxidation potential may lead to the enrichment of CH₄ emissions under the hydrological alterations, and reduced nitrification and denitrification potential contributed to the reduction of N₂O fluxes under all the treatments. Our study indicates that continuous flooding could curb the contribution of riparian GHGs fluxes to global warming but that the combination of N and P additions may increase the greenhouse effect mainly by regulating the CO₂ emissions of growing season in riparian ecosystem.

Verrucomicrobial methanotrophs: ecophysiology of metabolically versatile acidophiles

Methanotrophs are an important group of microorganisms that counteract methane emissions to the atmosphere. Methane-oxidising bacteria of the Alpha- and Gammaproteobacteria have been studied for over a century, while methanotrophs of the phylum Verrucomicrobia are a more recent discovery. Verrucomicrobial methanotrophs are extremophiles that live in very acidic geothermal ecosystems. Currently, more than a dozen strains have been isolated, belonging to the genera Methylacidiphilum and Methylacidimicrobium. Initially, these methanotrophs were thought to be metabolically confined. However, genomic analyses and physiological and biochemical experiments over the past years revealed that verrucomicrobial methanotrophs, as well as proteobacterial methanotrophs, are much more metabolically versatile than previously assumed. Several inorganic gases and other molecules present in acidic geothermal ecosystems can be utilised, such as methane, hydrogen gas, carbon dioxide, ammonium, nitrogen gas and perhaps also hydrogen sulfide. Verrucomicrobial methanotrophs could therefore represent key players in multiple volcanic nutrient cycles and in the mitigation of greenhouse gas emissions from geothermal ecosystems. Here, we summarise the current knowledge on verrucomicrobial methanotrophs with respect to their metabolic versatility and discuss the factors that determine their diversity in their natural environment. In addition, key metabolic, morphological and ecological characteristics of verrucomicrobial and proteobacterial methanotrophs are reviewed.

The role of humic substances in mitigating greenhouse gases emissions: Current knowledge and research gaps

Humic substances (HS) constitute a highly transformed fraction of natural organic matter (NOM) with a heterogeneous structure, which is rich in electron-transferring functional moieties. Because of this feature, HS display a versatile reactivity with a diversity of environmentally relevant organic and inorganic compounds either by abiotic or microbial processes. Consequently, extensive research has been conducted related to the potential of HS to drive relevant processes in bio-engineered systems, as well as in the biogeochemical cycling of key elements in natural environments. Nevertheless, the increase in the number of reports examining the relationship between HS and the microorganisms related to the production and consumption of greenhouse gases (GHG), the main drivers of global warming, has just emerged in the last years. In this paper, we discuss the importance of HS, and their analogous redox-active organic molecules (RAOM), on controlling the emission of three of the most relevant GHG due to their tight relationship with microbial activity, their abundance on the Earth's atmosphere, and their important global warming potentials: carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O). The current knowledge gaps concerning the microbial component, on-site occurrence, and environmental constraints affecting these HS-mediated processes are provided. Furthermore, strategies involving the metabolic traits that GHG-consuming/HS-reducing and -oxidizing microbes display for the development of environmental engineered processes are also discussed.

Environmental and Microbial Interactions Shape Methane-Oxidizing Bacterial Communities in a Stratified Lake

In stratified lakes, methane-oxidizing bacteria (MOB) are strongly mitigating methane fluxes to the atmosphere by consuming methane entering the water column from the sediments. MOB communities in lakes are diverse and vertically structured, but their spatio-temporal dynamics along the water column as well as physico-chemical parameters and interactions with other bacterial species that drive the community assembly have so far not been explored in depth. Here, we present a detailed investigation of the MOB and bacterial community composition and a large set of physico-chemical parameters in a shallow, seasonally stratified, and sub-alpine lake. Four highly resolved vertical profiles were sampled in three different years and during various stages of development of the stratified water column. Non-randomly assembled MOB communities were detected in all compartments. We could identify methane and oxygen gradients and physico-chemical parameters like pH, light, available copper and iron, and total dissolved nitrogen as important drivers of the MOB community structure. In addition, MOB were well-integrated into a bacterial-environmental network. Partial redundancy analysis of the relevance network of physico-chemical variables and bacteria explained up to 84% of the MOB abundances. Spatio-temporal MOB community changes were 51% congruent with shifts in the total bacterial community and 22% of variance in MOB abundances could be explained exclusively by the bacterial community composition. Our results show that microbial interactions may play an important role in structuring the MOB community along the depth gradient of stratified lakes.

Facultative methanotrophs - diversity, genetics, molecular ecology and biotechnological potential: a mini-review

Methane-oxidizing bacteria (methanotrophs) play a vital role in reducing atmospheric methane emissions, and hence mitigating their potent global warming effects. A significant proportion of the methane released is thermogenic natural gas, containing associated short-chain alkanes as well as methane. It was one hundred years following the description of methanotrophs that facultative strains were discovered and validly described. These can use some multi-carbon compounds in addition to methane, often small organic acids, such as acetate, or ethanol, although Methylocella strains can also use short-chain alkanes, presumably deriving a competitive advantage from this metabolic versatility. Here, we review the diversity and molecular ecology of facultative methanotrophs. We discuss the genetic potential of the known strains and outline the consequent benefits they may obtain. Finally, we review the biotechnological promise of these fascinating microbes.

Multiheme hydroxylamine oxidoreductases produce NO during ammonia oxidation in methanotrophs

Aerobic and nitrite-dependent methanotrophs make a living from oxidizing methane via methanol to carbon dioxide. In addition, these microorganisms cometabolize ammonia due to its structural similarities to methane. The first step in both of these processes is catalyzed by methane monooxygenase, which converts methane or ammonia into methanol or hydroxylamine, respectively. Methanotrophs use methanol for energy conservation, whereas toxic hydroxylamine is a potent inhibitor that needs to be rapidly removed. It is suggested that many methanotrophs encode a hydroxylamine oxidoreductase (mHAO) in their genome to remove hydroxylamine, although biochemical evidence for this is lacking. HAOs also play a crucial role in the metabolism of aerobic and anaerobic ammonia oxidizers by converting hydroxylamine to nitric oxide (NO). Here, we purified an HAO from the thermophilic verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV and characterized its kinetic properties. This mHAO possesses the characteristic P460 chromophore and is active up to at least 80 °C. It catalyzes the rapid oxidation of hydroxylamine to NO. In methanotrophs, mHAO efficiently removes hydroxylamine, which severely inhibits calcium-dependent, and as we show here, lanthanide-dependent methanol dehydrogenases, which are more prevalent in the environment. Our results indicate that mHAO allows methanotrophs to thrive under high ammonia concentrations in natural and engineered ecosystems, such as those observed in rice paddy fields, landfills, or volcanic mud pots, by preventing the accumulation of inhibitory hydroxylamine. Under oxic conditions, methanotrophs mainly oxidize ammonia to nitrite, whereas in hypoxic and anoxic environments reduction of both ammonia-derived nitrite and NO could lead to nitrous oxide (N2O) production.