The Amazon ecosystem plays a vital role in global climate regulation and biodiversity conservation but faces escalating threats from deforestation and degradation. The resulting secondary forests (SFs) provide a promising opportunity for Transformative Territorial Management, fostering restoration and enhancing conservation values. This study evaluated aboveground biomass (AGB), species diversity, forest structure, and soil properties in SFs of the Colombian Amazon along a chronosequence, from early to mature successional stages, in landscapes of mountains and of hills to identify key indicators for effective restoration management. The results show a consistent increase in AGB, species diversity, forest structure, and soil quality with forest age, though recovery patterns varied between both landscapes evaluated. Topographic differences influenced successional dynamics, with mountainous landscapes showing faster early recovery compared to the steadier, linear growth observed in hill areas. In hills, AGB at 10 years reached 12.65% of the biomass expected in a mature forest, increasing to nearly 42% by 40 years of abandonment, at a rate of 0.708 Mg C ha⁻¹ year⁻¹. In contrast, in the mountain landscape, AGB at 10 years reached approximately 8.35% of the carbon in a mature forest and increased to nearly 63.55% at 40 years. Forest age and soil properties emerged as primary drivers of AGB recovery, while diversity and forest structure played indirect but significant roles. In hill areas, soil conservation practices are critical for maintaining steady growth, whereas mountain regions benefit from assisted natural regeneration (ANR) to accelerate recovery. These findings highlight the importance of prioritizing the management of SFs as a central strategy for achieving restoration goals. Such practices are essential to enhance the ecological resilience of SFs and ensure their long-term sustainability, fostering their role as key contributors to restoration efforts and the provision of ecosystem services.

This study evaluated soil–atmosphere greenhouse gas (GHG) fluxes—including carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O)—in cacao agroecosystems on São Tomé Island, Central Africa. The field campaign was conducted between April and May 2025, coinciding with the transition from the short rainy season to the onset of the dry period. The sampling design comprised two system types (biodiverse and conventional), two crop development stages (growing and productive), and two climatic zones (wet and dry). Gas fluxes were measured using the static chamber method and analyzed in relation to climatic, topographic, and edaphic variables. CO₂ fluxes were the dominant contributor to total emissions, accounting for approximately 97.4% of the global warming potential (GWP), while CH₄ and N₂O together contributed less than 3%. The highest CO₂ emissions occurred in conventional systems during the growing stage in the wet zone (125.5 ± 11.41 mg C m⁻² h⁻¹). CH₄ generally acted as a sink, particularly in conventional systems in the dry zone (−12.58 ± 2.35 μg C m⁻² h⁻¹), although net emissions were detected in biodiverse systems in the wet zone (5.08 ± 1.50 μg C m⁻² h⁻¹). The highest N₂O fluxes were observed in conventional growing systems (32.28 ± 5.76 μg N m⁻² h⁻¹). GHG dynamics were mainly regulated by climatic factors—such as air temperature, relative humidity, and precipitation—and by key edaphic properties, including soil pH, soil organic carbon, soil temperature, and clay content. Projected GWP values ranged from 9.05 ± 2.77 to 40.9 ± 6.23 Mg CO₂-eq ha⁻¹ year⁻¹, with the highest values recorded in conventional systems in the growing stage. Overall, our findings underscore the potential of biodiversity-based agroforestry as a climate-smart practice to mitigate net GHG emissions in tropical cacao landscapes.

The expansion of conventional agricultural models in the Colombian Amazon has caused deforestation, biodiversity loss, and socio-environmental degradation. In response, agroecology and bioeconomy are emerging as key strategies to regenerate landscapes and foster sustainable production systems. We evaluated the agroecological performance of 25 farms in the Andean–Amazon transition zone of Colombia using FAO’s Tool for Agroecology Performance Evaluation (TAPE). The analysis included land cover dynamics (2002–2024), characterization of the agroecological transition based on the 10 Elements of Agroecology, and 23 economic, environmental, and social indicators. Four farm typologies were identified; among them, Mixed Family Farms (MFF) achieved the highest transition score (CAET = 60.5%) and excelled in crop diversity (64%), soil health (SHI = 4.24), productive autonomy (VA/GVP = 0.69), and household empowerment (FMEF= 85%). Correlation analyses showed strong links between agroecological practices, economic efficiency, and social cohesion. Land cover dynamics revealed a continuous decline in forest cover (12.9% in 2002 to 7.1% in 2024) and an increase in secondary vegetation, underscoring the urgent need for restorative approaches. Overall, farms further along the agroecological transition were more productive, autonomous, and socially cohesive, strengthening territorial resilience. The application of TAPE proved robust multidimensional evidence to support agroecological monitoring and decision-making, with direct implications for land use planning, rural development strategies, and sustainability policies in the Amazon. At the same time, its sensitivity to high baseline biodiversity and to the complex socio-ecological dynamics of the Colombian Amazon underscores the need to refine the methodology in future applications. By addressing these challenges, the study contributes to the broader international debate on agroecological transitions, offering insights relevant for other tropical frontiers and biodiversity-rich regions facing similar pressures.

This study evaluated the seasonal variability of soil–atmosphere greenhouse gas (GHG) fluxes—carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O)—across a land-use gradient in the Andean–Amazon transition zone of Colombia. The gradient included five land-use types incorporating at least one innovative climate-smart prac-tice—improved pasture (IP), cacao agroforestry system (CaAS), copoazu agroforestry system (CoAS), secondary forest with agroforestry enrichment (SFAE), and moriche palm swamp ecosystem (MPSE)—alongside the dominant regional land uses, old-growth forest (OF) and degraded pasture (DP). Soil GHG fluxes varied markedly among land-use types and between seasons. CO₂ fluxes were consistently higher during the dry season, whereas CH₄ and N₂O fluxes peaked in the rainy season. Agroecological and restoration systems exhibited substantially lower CO₂ emissions (7.34–9.74 Mg CO₂-C ha⁻¹ yr⁻¹) compared with DP (18.85 Mg CO₂-C ha⁻¹ yr⁻¹) during the rainy season, and lower N₂O fluxes (0.21–1.04 Mg CO₂-C ha⁻¹ yr⁻¹) during the dry season. In contrast, the MPSE presented high CH₄ emissions in the rainy season (300.45 kg CH₄-C ha⁻¹ yr⁻¹). Across all land uses, CO₂ was the dominant contributor to the total GWP (> 95% of emissions). The highest global warming potential (GWP) occurred in DP, whereas CaAS, CoAS and MPSE exhibited the lowest values. Soil temperature, pH, exchangeable acidity, texture, and bulk density play a decisive role in regulating GHG fluxes, whereas climatic factors, such as air temperature and relative humidity, influenced fluxes indirectly by modulating soil conditions. These findings underscore the role of diversified agroforestry and restoration systems in mit-igating GHG emissions and the need to integrate soil and climate drivers into regional climate models.

This study evaluated the seasonal variability of soil–atmosphere greenhouse gas (GHG) fluxes—carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O)—across a land-use gradient in the Andean–Amazon transition zone of Colombia. The gradient included five land-use types incorporating at least one innovative climate-smart practice—improved pasture (IP), cacao agroforestry system (CaAS), copoazu agroforestry system (CoAS), secondary forest with agroforestry enrichment (SFAE), and moriche palm swamp ecosystem (MPSE)—alongside the dominant regional land uses, old-growth forest (OF) and degraded pasture (DP). Soil GHG fluxes varied markedly among land-use types and between seasons. CO₂ fluxes were consistently higher during the dry season, whereas CH₄ and N₂O fluxes peaked in the rainy season. Agroecological and restoration systems exhibited substantially lower CO₂ emissions (7.34–9.74 Mg CO₂-C ha⁻¹ yr⁻¹) compared with DP (18.85 Mg CO₂-C ha⁻¹ yr⁻¹) during the rainy season, and lower N₂O fluxes (0.21–1.04 Mg CO₂-C ha⁻¹ yr⁻¹) during the dry season. In contrast, the MPSE presented high CH₄ emissions in the rainy season (300.45 kg CH₄-C ha⁻¹ yr⁻¹). Across all land uses, CO₂ was the dominant contributor to the total GWP (>95% of emissions). The highest global warming potential (GWP) occurred in DP, whereas CaAS, CoAS and MPSE exhibited the lowest values. Soil temperature, pH, exchangeable acidity, texture, and bulk density play a decisive role in regulating GHG fluxes, whereas climatic factors, such as air temperature and relative humidity, influence fluxes indirectly by modulating soil conditions. These findings underscore the role of diversified agroforestry and restoration systems in mitigating GHG emissions and the need to integrate soil and climate drivers into regional climate models.