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Denitrification – a key process in the global nitrogen cycle and main source of the greenhouse gas N2O – is intricately controlled by O2. While the transition from aerobic respiration to denitrification is well-studied, our understanding of denitrifier communities' responses to cyclic oxic/anoxic shifts, prevalent in natural and engineered systems, is limited. Here, agricultural soil is exposed to repeated cycles of long or short anoxic spells (LA; SA) or constant oxic conditions (Ox). Surprisingly, denitrification and N2O reduction rates are three times greater in Ox than in LA and SA during a final anoxic incubation, despite comparable bacterial biomass and denitrification gene abundances. Metatranscriptomics indicate that LA favors canonical denitrifiers carrying nosZ clade I. Ox instead favors nosZ clade II-carrying partial- or non-denitrifiers, suggesting efficient partnering of the reduction steps among organisms. SA has the slowest denitrification progression and highest accumulation of intermediates, indicating less functional coordination. The findings demonstrate how adaptations of denitrifier communities to varying O2 conditions are tightly linked to the duration of anoxic episodes, emphasizing the importance of knowing an environment's O2 legacy for accurately predicting N2O emissions originating from denitrification. A soil history of constant oxygen exposure enhances N2O reduction rates under anoxia compared to a history of long or short anoxic pulses, highlighting the importance of knowing the oxygen legacy of a soil for accurate N2O emission predictions. [ABSTRACT FROM AUTHOR]

Members of the order Methanomicrobiales are abundant, and sometimes dominant, hydrogenotrophic (H2-CO2 utilizing) methanoarchaea in a broad range of anoxic habitats. Despite their key roles in greenhouse gas emissions and waste conversion to methane, little is known about the physiological and genomic bases for their widespread distribution and abundance. In this study, we compared the genomes of nine diverse Methanomicrobiales strains, examined their pangenomes, reconstructed gene flow and identified genes putatively mediating their success across different habitats. Most strains slowly increased gene content whereas one, Methanocorpusculum labreanum, evidenced genome downsizing. Peat-dwelling Methanomicrobiales showed adaptations centered on improved transport of scarce inorganic nutrients and likely use H+ rather than Na+ transmembrane chemiosmotic gradients during energy conservation. In contrast, other Methanomicrobiales show the potential to concurrently use Na+ and H+ chemiosmotic gradients. Analyses also revealed that the Methanomicrobiales lack a canonical electron bifurcation system (MvhABGD) known to produce low potential electrons in other orders of hydrogenotrophic methanogens. Additional putative differences in anabolic metabolism suggest that the dynamics of interspecies electron transfer from Methanomicrobiales syntrophic partners can also differ considerably. Altogether, these findings suggest profound differences in electron trafficking in the Methanomicrobiales compared with other hydrogenotrophs, and warrant further functional evaluations.

Here, we report the complete genome sequence (2.92 Mb) of Methanosphaerula palustris E1-9C(T), a methanogen isolated from a minerotrophic fen. This is the first genome report of the Methanosphaerula genus, within the Methanoregulaceae family, in the Methanomicrobiales order. E1-9C(T) relatives are found in a wide range of ecological and geographical settings.

1. Nutrients are a critical resource for plant growth, but the elements limiting growth in tropical forests have rarely been determined. 2. We investigated the influence of nitrogen (N), phosphorus (P), potassium (K) and micronutrients on seedling biomass and nutrient allocation in a factorial nutrient fertilization experiment in lowland tropical forest at the Barro Colorado Nature Monument, Panama. We also measured 8 years of herbivory and growth for 1800 seedlings. We sought to determine the identity of limiting elements and possible nutrient interactions. 3. The five study species were Alseis blackiana, Desmopsis panamensis, Heisteria concinna, Sorocea affinis and Tetragastris panamensis. Plants grew in deeply shaded understorey with a mean canopy openness of 4.9% (±0.7%; 1 SE). 4. Tissue N concentration increased by 11% with N addition. Tissue P concentration increased by 16% with P addition. Tissue K increased by 4% with K addition. K addition reduced root‐to‐shoot biomass ratio. There was no significant effect of fertilization on specific leaf area or leaf area ratio. 5. The proportion of leaves damaged and the mean level of damage by herbivory increased with P and K addition and showed a significant P × K interaction. 6.7ensp;Across all species and years, relative growth rate of height increased with K addition and with N and P in combination. Relative growth rate of leaf count trended 8.5% higher with K addition (P = 0.076). 7. We also added micronutrients in a parallel experiment. There was no effect of micronutrient addition on any seedling parameter. 8. Synthesis. K addition affected seedlings by enhancing tissue nutrient concentration, increasing herbivory, reducing root‐to‐shoot biomass ratio and increasing height growth. Additional effects of N or P on tissue chemistry, herbivory and growth offer support for the multiple limiting resources hypothesis. Our results suggest that seedling growth is limited by nutrients, especially K, even under highly shaded conditions in this lowland tropical forest.

We maintained a factorial nitrogen (N), phosphorus (P), and potassium (K) addition experiment for 11 years in a humid lowland forest growing on a relatively fertile soil in Panama to evaluate potential nutrient limitation of tree growth rates, fine-litter production, and fine-root biomass. We replicated the eight factorial treatments four times using 32 plots of 40 x 40 m each. The addition of K was associated with significant decreases in stand-level fine-root biomass and, in a companion study of seedlings, decreases in allocation to roots and increases in height growth rates. The addition of K and N together was associated with significant increases in growth rates of saplings and poles (1-10 cm in diameter at breast height) and a further marginally significant decrease in stand-level fine-root biomass. The addition of P was associated with a marginally significant (P = 0.058) increase in fine-litter production that was consistent across all litter fractions. Our experiment provides evidence that N, P, and K all limit forest plants growing on a relatively fertile soil in the lowland tropics, with the strongest evidence for limitation by K among seedlings, saplings, and poles.