Smallholder-dominated agricultural mosaic landscapes are highlighted as model production systems that deliver both economic and ecological goods in tropical agricultural landscapes, but trade-offs underlying current land-use dynamics are poorly known. Here, using the most comprehensive quantification of land-use change and associated bundles of ecosystem functions, services and economic benefits to date, we show that Indonesian smallholders predominantly choose farm portfolios with high economic productivity but low ecological value. The more profitable oil palm and rubber monocultures replace forests and agroforests critical for maintaining above- and below-ground ecological functions and the diversity of most taxa. Between the monocultures, the higher economic performance of oil palm over rubber comes with the reliance on fertilizer inputs and with increased nutrient leaching losses. Strategies to achieve an ecological-economic balance and a sustainable management of tropical smallholder landscapes must be prioritized to avoid further environmental degradation.

Prokaryotes are the most abundant and diverse group of microorganisms in soil and mediate virtually all biogeochemical cycles in terrestrial ecosystems. Thereby, they influence aboveground plant productivity and diversity. In this study, the impact of rainforest transformation to intensively managed cash crop systems on soil prokaryotic communities was investigated. The studied managed land use system comprised rubber agroforests (jungle rubber), rubber plantation and oil plantations within two Indonesian landscapes Bukit Duabelas and Harapan. Soil prokaryotic community composition and diversity were assessed by pyrotag sequencing of bacterial and archaeal 16S rRNA genes. The curated dataset contained 20,494 bacterial and 1,762 archaeal Operational Taxonomic Units at species level (97% genetic identity). Analysis revealed changes in indigenous taxon-specific patterns of soil prokaryotic communities accompanying lowland rainforest transformation to jungle rubber, and intensively managed rubber and oil palm plantations. Distinct clustering of the rainforest soil communities indicated that these are different from the communities in the studied managed land use systems. The predominant bacterial taxa in all investigated soils were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Overall, the bacterial community shifted from proteobacterial groups in rainforest soils to Acidobacteria in managed soils. The archaeal soil communities were mainly represented by Thaumarchaeota and Euryarchaeota. Members of the Terrestrial Group and South African Gold Mine Group 1 (Thaumarchaeota) dominated in the rainforest and members of Thermoplasmata in the managed land use systems. The alpha and beta diversity of the soil prokaryotic communities was higher in managed land use systems than in rainforest. In the case of bacteria, this was related to soil characteristics such as pH value, exchangeable Ca and Fe content, C to N ratio, and extractable P content. Archaeal community composition and diversity were correlated to pH value, exchangeable Fe content, water content, and total N. The distribution of bacterial and archaeal taxa involved in biological N cycle indicated functional shifts of the cycle during conversion of rainforest to plantations.

Conversion of forest to rubber and oil palm plantations is widespread in Sumatra, Indonesia, and it is largely unknown how such land-use conversion affects nutrient leaching losses. Our study aimed to quantify nutrient leaching and nutrient retention efficiency in the soil after land-use conversion to smallholder rubber and oil palm plantations. In Jambi province, Indonesia, we selected two landscapes on highly weathered Acrisol soils that mainly differed in texture: loam and clay. Within each soil type, we compared two reference land uses, lowland forest and jungle rubber (defined as rubber trees interspersed in secondary forest), with two converted land uses: smallholder rubber and oil palm plantations. Within each soil type, the first three land uses were represented by 4 replicate sites and the oil palm by three sites, totaling 30 sites. We measured leaching losses using suction cup lysimeters sampled biweekly to monthly from February to December 2013. Forests and jungle rubber had low solute concentrations in drainage water, suggesting low internal inputs of rock-derived nutrients and efficient internal cycling of nutrients. These reference land uses on the clay Acrisol soils had lower leaching of dissolved N and base cations (P = 0.01–0.06) and higher N and base cation retention efficiency (P < 0.01–0.07) than those on the loam Acrisols. In the converted land uses, particularly on the loam Acrisol, the fertilized area of oil palm plantations showed higher leaching of dissolved N, organic C, and base cations (P < 0.01–0.08) and lower N and base cation retention efficiency compared to all the other land uses (P < 0.01–0.06). The unfertilized rubber plantations, particularly on the loam Acrisol, showed lower leaching of dissolved P (P = 0.08) and organic C (P < 0.01) compared to forest or jungle rubber, reflecting decreases in soil P stocks and C inputs to the soil. Our results suggest that land-use conversion to rubber and oil palm causes disruption of initially efficient nutrient cycling, which decreases nutrient availability. Over time, smallholders will likely be increasingly reliant on fertilization, with the risk of diminishing water quality due to increased nutrient leaching. Thus, there is a need to develop management practices to minimize leaching while sustaining productivity.

Oil palm (Elaeis guineensis) and rubber (Hevea brasiliensis) plantations cover large areas of former rainforest in Sumatra, Indonesia, supplying the global demand for these crops. Although forest conversion is known to influence soil nitrous oxide (N₂O) and nitric oxide (NO) fluxes, measurements from oil palm and rubber plantations are scarce (for N₂O) or nonexistent (for NO). Our study aimed to (1) quantify changes in soil–atmosphere fluxes of N oxides with forest conversion to rubber and oil palm plantations and (2) determine their controlling factors. In Jambi, Sumatra, we selected two landscapes that mainly differed in texture but were both on heavily weathered soils: loam and clay Acrisol soils. Within each landscape, we investigated lowland forests, rubber trees interspersed in secondary forest (termed as jungle rubber), both as reference land uses and smallholder rubber and oil palm plantations as converted land uses. In the loam Acrisol landscape, we conducted a follow-on study in a large-scale oil palm plantation (called PTPN VI) for comparison of soil N₂O fluxes with smallholder oil palm plantations. Land-use conversion to smallholder plantations had no effect on soil N-oxide fluxes (P = 0. 58 to 0.76) due to the generally low soil N availability in the reference land uses that further decreased with land-use conversion. Soil N₂O fluxes from the large-scale oil palm plantation did not differ with those from smallholder plantations (P = 0. 15). Over 1-year measurements, the temporal patterns of soil N-oxide fluxes were influenced by soil mineral N and water contents. Across landscapes, annual soil N₂O emissions were controlled by gross nitrification and sand content, which also suggest the influence of soil N and water availability. Soil N₂O fluxes (µg N m⁻² h⁻¹) were 7 ± 2 to 14 ± 7 (reference land uses), 6 ± 3 to 9 ± 2 (rubber), 12 ± 3 to 12 ± 6 (smallholder oil palm) and 42 ± 24 (large-scale oil palm). Soil NO fluxes (µg N m⁻² h⁻¹) were −0.6 ± 0.7 to 5.7 ± 5.8 (reference land uses), −1.2 ± 0.5 to −1.0 ± 0.2 (rubber) and −0.2 ± 1.2 to 0.7 ± 0.7 (smallholder oil palm). To improve the estimate of soil N-oxide fluxes from oil palm plantations in this region, studies should focus on large-scale plantations (which usually have 2 to 4 times higher N fertilization rates than smallholders) with frequent measurements following fertilizer application.