Ammonium influences kinetics and structure of methanotrophic consortia

Resilience of aerobic methanotrophs in soils; spotlight on the methane sink under agriculture

Aerobic methanotrophs are a specialized microbial group, catalyzing the oxidation of methane. Disturbance-induced loss of methanotroph diversity/abundance, thus results in the loss of this biological methane sink. Here, we synthesized and conceptualized the resilience of the methanotrophs to sporadic, recurring, and compounded disturbances in soils. The methanotrophs showed remarkable resilience to sporadic disturbances, recovering in activity and population size. However, activity was severely compromised when disturbance persisted or reoccurred at increasing frequency, and was significantly impaired following change in land use. Next, we consolidated the impact of agricultural practices after land conversion on the soil methane sink. The effects of key interventions (tillage, organic matter input, and cover cropping) where much knowledge has been gathered were considered. Pairwise comparisons of these interventions to nontreated agricultural soils indicate that the agriculture-induced impact on the methane sink depends on the cropping system, which can be associated to the physiology of the methanotrophs. The impact of agriculture is more evident in upland soils, where the methanotrophs play a more prominent role than the methanogens in modulating overall methane flux. Although resilient to sporadic disturbances, the methanotrophs are vulnerable to compounded disturbances induced by anthropogenic activities, significantly affecting the methane sink function.

Interkingdom interaction: the soil isopod Porcellio scaber stimulates the methane-driven bacterial and fungal interaction

Porcellio scaber (woodlice) are (sub-)surface-dwelling isopods, widely recognized as "soil bioengineers", modifying the edaphic properties of their habitat, and affecting carbon and nitrogen mineralization that leads to greenhouse gas emissions. Yet, the impact of soil isopods on methane-cycling processes remains unknown. Using P. scaber as a model macroinvertebrate in a microcosm study, we determined how the isopod influences methane uptake and the associated interaction network in an agricultural soil. Stable isotope probing (SIP) with 13C-methane was combined to a co-occurrence network analysis to directly link activity to the methane-oxidizing community (bacteria and fungus) involved in the trophic interaction. Compared to microcosms without the isopod, P. scaber significantly induced methane uptake, associated to a more complex bacteria-bacteria and bacteria-fungi interaction, and modified the soil nutritional status. Interestingly, 13C was transferred via the methanotrophs into the fungi, concomitant to significantly higher fungal abundance in the P. scaber-impacted soil, indicating that the fungal community utilized methane-derived substrates in the food web along with bacteria. Taken together, results showed the relevance of P. scaber in modulating methanotrophic activity with implications for bacteria-fungus interaction.

Effects of abrupt and gradual increase of atmospheric CO2 concentration on methanotrophs in paddy fields

The simulation of abrupt atmospheric CO₂ increase is a common way to examine the response of soil methanotrophs to future climate change. However, atmosphere is undergoing a gradual CO₂ increase, and it is unknown whether the previously reported response of methanotrophs to abrupt CO₂ increase can well represent their response to the gradual increase. To improve the understanding of the effect of elevated CO₂ (eCO₂) on methanotrophs in paddy ecosystems, the methane oxidation potential and communities of methanotrophs were examined via open top chambers under the three following CO₂ treatments: an ambient CO₂ concentration (AC); an abrupt CO₂ increase by 200 ppm above AC (AI); a gradual CO₂ increase by 40 ppm each year until 200 ppm above AC (GI). Relative to AC treatment, AI and GI treatments significantly (p < 0.05) increased the methane oxidation rate by 43.8% and 36.7%, respectively, during rice growth period. Furthermore, the abundance of pmoA genes was significantly (p < 0.05) increased by 62.4% and 32.5%, respectively, under AI and GI treatments. However, there were no significant variations in oxidation rate or gene abundance between the two eCO₂ treatments. In addition, no obvious change of overall community composition of methanotrophs was observed among treatments, while the proportions of Methylosarcina and Methylocystis significantly (p < 0.05) changed. Taken together, our results indicate similar response of methanotrophs to abrupt and gradual CO₂ increase, although the magnitude of response under gradual increase was smaller and the abrupt increase may somewhat overestimate the response.

Methylocystis sp. Strain SC2 Acclimatizes to Increasing NH4+ Levels by a Precise Rebalancing of Enzymes and Osmolyte Composition

A high NH₄⁺ load is known to inhibit bacterial methane oxidation. This is due to a competition between CH₄ and NH₃ for the active site of particulate methane monooxygenase (pMMO), which converts CH₄ to CH₃OH. Here, we combined global proteomics with amino acid profiling and nitrogen oxides measurements to elucidate the cellular acclimatization response of Methylocystis sp. strain SC2 to high NH₄⁺ levels. Relative to 1 mM NH₄⁺, a high (50 mM and 75 mM) NH₄⁺ load under CH₄-replete conditions significantly increased the lag phase duration required for proteome adjustment. The number of differentially regulated proteins was highly significantly correlated with an increasing NH₄⁺ load. The cellular responses to increasing ionic and osmotic stress involved a significant upregulation of stress-responsive proteins, the K⁺ "salt-in" strategy, the synthesis of compatible solutes (glutamate and proline), and the induction of the glutathione metabolism pathway. A significant increase in the apparent K_m value for CH₄ oxidation during the growth phase was indicative of increased pMMO-based oxidation of NH₃ to toxic hydroxylamine. The detoxifying activity of hydroxlyamine oxidoreductase (HAO) led to a significant accumulation of NO₂^- and, upon decreasing O₂ tension, N₂O. Nitric oxide reductase and hybrid cluster proteins (Hcps) were the candidate enzymes for the production of N₂O. In summary, strain SC2 has the capacity to precisely rebalance enzymes and osmolyte composition in response to increasing NH₄⁺ exposure, but the need to simultaneously combat both ionic-osmotic stress and the toxic effects of hydroxylamine may be the reason why its acclimatization capacity is limited to 75 mM NH₄⁺. IMPORTANCE In addition to reducing CH₄ emissions from wetlands and landfills, the activity of alphaproteobacterial methane oxidizers of the genus Methylocystis contributes to the sink capacity of forest and grassland soils for atmospheric methane. The methane-oxidizing activity of Methylocystis spp. is, however, sensitive to high NH₄⁺ concentrations. This is due to the competition of CH₄ and NH₃ for the active site of particulate methane monooxygenase, thereby resulting in the production of toxic hydroxylamine with an increasing NH₄⁺ load. An understanding of the physiological and molecular response mechanisms of Methylocystis spp. is therefore of great importance. Here, we combined global proteomics with amino acid profiling and NOx measurements to disentangle the cellular mechanisms underlying the acclimatization of Methylocystis sp. strain SC2 to an increasing NH₄⁺ load.

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.

Proteinaceous methanotrophs for feed additive using biowaste as carbon and nutrients source

To achieve a sustainable production of food and feed production, inexpensive carbon and nutrient sources are needed. In the present study, biologically upgraded biogas is coupled with electrochemically extracted nitrogen from digested biowaste to cultivate mixed methanotrophs as protein source. Results showed that an increase from less than 5 μgCu²⁺/L to 100 μgCu²⁺/L increased the biomass production by 41%. Microbial analysis revealed that the dominated Methylomonas spp. followed by Methylophilus spp. created a specialized community for high CH₄ assimilation. Moreover, duplicate semi-continuous fermenters run for 120 days validating the efficiency of alternative carbon and nitrogen feedstocks at long-term operation. As for dry cell weight (DCW) production, more than 2.5 g-DCW/L were produced using biologically upgraded biogas and electrochemically extracted nitrogen. Furthermore, the protein content and amino acid profile (>50% of DCW) demonstrated that the microbial biomass pose the characteristics to be used as animal feed additive.