New particle formation (NPF) in the tropical upper troposphere is a globally important source of atmospheric aerosols^1–4. It is known to occur over the Amazon basin, but the nucleation mechanism and chemical precursors have yet to be identified². Here we present comprehensive in situ aircraft measurements showing that extremely low-volatile oxidation products of isoprene, particularly certain organonitrates, drive NPF in the Amazonian upper troposphere. The organonitrates originate from OH-initiated oxidation of isoprene from forest emissions in the presence of nitrogen oxides from lightning. Nucleation bursts start about 2 h after sunrise in the outflow of nocturnal deep convection, producing high aerosol concentrations of more than 50,000 particles cm^{− 3}. We report measurements of characteristic diurnal cycles of precursor gases and particles. Our observations show that the interplay between biogenic isoprene, deep tropical convection with associated lightning, oxidation photochemistry and the low ambient temperature uniquely promotes NPF. The particles grow over time, undergo long-range transport and descend through subsidence to the lower troposphere, in which they can serve as cloud condensation nuclei (CCN) that influence the Earth’s hydrological cycle, radiation budget and climate^1,4–8.

The Amazon rainforest is the largest source of biogenic volatile organic compounds (BVOCs) to the atmosphere. To understand the distribution and chemistry of BVOCs, airborne and ground-based measurements of BVOCs are conducted over the Amazon rainforest in the CAFE-Brazil campaign (December 2022–January 2023), including diel (24-hour) profiles between 0.3-14 km for isoprene, its oxidation products, and total monoterpenes. Although daytime deep convective transport of BVOCs is rendered ineffective by photochemical loss, nocturnal deep-convection exports considerable BVOC quantities to high altitudes, extending the chemical influence of the rainforest to the upper troposphere, and priming it for rapid organic photochemistry and particle formation at dawn. After contrasting pristine and deforested areas, a BVOC sensitivity analysis is performed using a chemistry-climate model. Here we show that reducing BVOC emissions, decreased upper tropospheric ozone, increased lower tropospheric hydroxyl radicals, shortened the methane lifetime, with the net effect of enhancing climate warming through ozone and aerosols.

Monoterpenes are key to plant communication and defence against biotic (e.g., herbivory) and abiotic (e.g., heat, drought) stress. Chiral monoterpenes, like alpha-pinene, exist as mirror image pairs, known as enantiomers. Enantiomers have the same atmospheric reactivity, but are produced and emitted by different enzymes and internal leaf mechanisms. Abiotic stress can alter their relative emissions, suggesting enantiomer ratios could indicate stress severity. Here we present (−)- and (+)-alpha-pinene and methyl salicylate measurements from the Amazon rainforest over time-of-day, season, and the 2023-24 El Niño. Correlations between alpha-pinene enantiomers shifted with stress, aligning with weakening carbon dioxide uptake by vegetation and transition between de novo and storage emissions. Low- and high-stress zones, along with a recovery zone, were defined through alpha-pinene enantiomer correlations, revealing a metric for ecosystem stress. This chiral ratio reveals diel, seasonal, El Niño, and edge effect stresses, offering a method to gauge drought severity due to climate change.

Lightning is the most important source of nitric oxide (NO) in the tropical upper troposphere and controls the formation of tropospheric ozone (). It is associated with deep convection and occurs mostly over continents. The Chemistry of the Atmosphere Field Experiment in the Pacific (CAFE Pacific) was conducted in early 2024 from Cairns, Australia, taking airborne measurements across the Australian continent and the surrounding maritime regions. Based on cloud top properties, lightning data and in situ observations of NO, and carbon monoxide, we show that deep convection occurs over Northern Australia and the Indo‐Pacific Warm Pool. While we identify strong lightning activity over Australia, we observe deep convection in the Warm Pool that is not electrified. Our observations of low in the Warm Pool can be attributed to ‐poor air from the marine boundary layer, which is not replenished by photochemical production from NO at high altitudes.

Lightning is the most important source of nitric oxide (NO) in the tropical upper troposphere and controls the formation of tropospheric ozone (O ₃ ). It is associated with deep convective processes and occurs mostly (∼90%) over tropical continents. The Chemistry of the Atmosphere Field Experiment in the Pacific (CAFE Pacific) was conducted in early 2024 from Cairns, Australia, taking airborne measurements across the Australian continent and the surrounding maritime regions. Based on cloud top properties, lightning data and in situ observations of NO, O ₃ and carbon monoxide (CO), we show that deep convection occurs over both Northern Australia and the Indo-Pacific Warm Pool. While we identify strong lightning activity over Australia, deep convection in the Warm Pool is not electrified. We conclude that low O ₃ in the Warm Pool is due to O ₃ -poor air from the marine boundary layer, which is not replenished by photochemical production from NO at high altitudes.