Agriculture significantly contributes to greenhouse gas (GHG) emissions, yet fluxes from irrigated semi-arid systems remain poorly quantified. This study investigates CO₂, CH₄, N₂O, and NH₃ fluxes in a short-term lettuce experiment under semi-arid conditions. The objective was to quantify flux variability and identify key environmental and management drivers. High-frequency soil gas flux measurements were conducted under three treatments: irrigated soil (I), irrigated soil with plants (IP), and irrigated soil with plants plus NH₄NO₃ fertilizer (IPF). Environmental factors, including solar radiation, soil temperature, water-filled pore space, and relative projected leaf area, were monitored. A Random Forest model identified main flux determinants. Fluxes varied with plant function, growth, and fertilization. IP exhibited net CO₂ uptake through photosynthesis, whereas I and IPF showed net CO₂ emissions from soil respiration and fertilizer-induced disruption of plant function, respectively. CH₄ uptake occurred across treatments but decreased with plant presence. Fertilization in IPF triggered episodic N₂O (EF = 0.1%) and NH₃ emissions (EF = 0.97%) linked to nitrogen input. Vegetated semi-arid soils can act as CO₂ sinks when nitrogen is optimally managed. Excess or poorly timed nitrogen delays CO₂ uptake and increases reactive nitrogen losses. Methanotrophic activity drives CH₄ dynamics and is influenced by plants and fertilization. Maintaining crop vigor and applying precision nitrogen management are essential to optimize productivity while mitigating GHG and NH₃ emissions in semi-arid lettuce cultivation.

Microbial communities drive the stabilisation of organic matter during manure storage; however, the combined influence of substrate origin and sudden rainfall occurrences on these communities remains poorly understood. For the first time in Cyprus, we investigated the effects of manure type (dairy cow vs. goat) and a drying–rainfall simulation pulse on the community composition, diversity, and functional potential during manure storage, using 16S rRNA metabarcoding and shotgun sequencing. Under dry conditions, substrate composition set the baseline, with the more structurally heterogeneous goat manure supporting significantly higher diversity than dairy cow manure. Rainfall simulation then acted as a dominant environmental filter, sharply reducing diversity and driving compositional convergence across manure types. This shift coincided with a rapid rise of fast‐responding, stress‐tolerant taxa, primarily Bacillota, and an increase in functions linked to sporulation and rapid growth. Ordination and dispersion analyses further showed that substrate origin modulates stability: after rainfall simulation, cow‐manure communities exhibited greater compositional displacement and greater variability than those from goat manure. Overall, the efficacy and stability of manure storage systems emerge from the interplay between initial physicochemical template and dynamic moisture stress. Optimising large‐scale operations will require management approaches that consider substrate characteristics, microbial community structure, and moisture dynamics.