Summary1. Agricultural intensification reduces ecological resilience of land-use systems, whereas paradoxically, environmental change and climate extremes require a higher response capacity than ever. Adaptation strategies to environmental change include maintenance of shade trees in tropical agroforestry, but conversion of shaded to unshaded systems is common practice to increase short-term yield. 2. In this paper, we review the short-term and long-term ecological benefits of shade trees in coffee Coffea arabica, C. canephora and cacao Theobroma cacao agroforestry and emphasize the poorly understood, multifunctional role of shade trees for farmers and conservation alike. 3. Both coffee and cacao are tropical understorey plants. Shade trees in agroforestry enhance functional biodiversity, carbon sequestration, soil fertility, drought resistance as well as weed and biological pest control. However, shade is needed for young cacao trees only and is less important in older cacao plantations. This changing response to shade regime with cacao plantation age often results in a transient role for shade and associated biodiversity in agroforestry. 4. Abandonment of old, unshaded cacao in favour of planting young cacao in new, thinned forest sites can be named 'short-term cacao boom-and-bust cycle', which counteracts tropical forest conservation. In a 'long-term cacao boom-and-bust cycle', cacao boom can be followed by cacao bust due to unmanageable pest and pathogen levels (e.g. in Brazil and Malaysia). Higher pest densities can result from physiological stress in unshaded cacao and from the larger cacao area planted. Risk-averse farmers avoid long-term vulnerability of their agroforestry systems by keeping shade as an insurance against insect pest outbreaks, whereas yield-maximizing farmers reduce shade and aim at short-term monetary benefits. 5. Synthesis and applications. Sustainable agroforestry management needs to conserve or create a diverse layer of multi-purpose shade trees that can be pruned rather than removed when crops mature. Incentives from payment-for-ecosystem services and certification schemes encourage farmers to keep high to medium shade tree cover. Reducing pesticide spraying protects functional *Correspondence author. E-mail: ttschar@gwdg.de 2011, 48, 619-629 doi: 10.1111/j.1365-2664.2010.01939.x Ó 2011 The Authors. Journal of Applied Ecology Ó 2011 British Ecological Society agrobiodiversity such as antagonists of pests and diseases, pollinating midges determining cacao yields and pollinating bees enhancing coffee yield. In a landscape perspective, natural forest alongside agroforestry allows noncrop-crop spillover of a diversity of functionally important organisms. Knowledge transfer between farmers, agronomists and ecologists in a participatory approach helps to encourage a shade management regime that balances economic and ecological needs and provides a 'diversified food-and-cash crop' livelihood strategy. Journal of Applied Ecology

Tropical lowland rainforests are increasingly threatened by the expansion of agriculture and the extraction of natural resources. In Jambi Province, Indonesia, the interdisciplinary EFForTS project focuses on the ecological and socio-economic dimensions of rainforest conversion to jungle rubber agroforests and monoculture plantations of rubber and oil palm. Our data confirm that rainforest transformation and land use intensification lead to substantial losses in biodiversity and related ecosystem functions, such as decreased above- and below-ground carbon stocks. Owing to rapid step-wise transformation from forests to agroforests to monoculture plantations and renewal of each plantation type every few decades, the converted land use systems are continuously dynamic, thus hampering the adaptation of animal and plant communities. On the other hand, agricultural rainforest transformation systems provide increased income and access to education, especially for migrant smallholders. Jungle rubber and rubber monocultures are associated with higher financial land productivity but lower financial labour productivity compared to oil palm, which influences crop choice: smallholders that are labour-scarce would prefer oil palm while land-scarce smallholders would prefer rubber. Collecting long-term data in an interdisciplinary context enables us to provide decision-makers and stakeholders with scientific insights to facilitate the reconciliation between economic interests and ecological sustainability in tropical agricultural landscapes.

Losses of biodiversity and ecosystem functioning due to rainforest destruction and agricultural intensification are prime concerns for science and society alike. Potentially, ecosystems show nonlinear responses to land-use intensification that would open management options with limited ecological losses but satisfying economic gains. However, multidisciplinary studies to quantify ecological losses and socioeconomic tradeoffs under different management options are rare. Here, we evaluate opposing land use strategies in cacao agroforestry in Sulawesi, Indonesia, by using data on species richness of nine plant and animal taxa, six related ecosystem functions, and on socioeconomic drivers of agroforestry expansion. Expansion of cacao cultivation by 230% in the last two decades was triggered not only by economic market mechanisms, but also by rarely considered cultural factors. Transformation from near-primary forest to agroforestry had little effect on overall species richness, but reduced plant biomass and carbon storage by Ϸ75% and species richness of forest-using species by Ϸ60%. In contrast, increased land use intensity in cacao agroforestry, coupled with a reduction in shade tree cover from 80% to 40%, caused only minor quantitative changes in biodiversity and maintained high levels of ecosystem functioning while doubling farmers' net income. However, unshaded systems further increased income by Ϸ40%, implying that current economic incentives and cultural preferences for new intensification practices put shaded systems at risk. We conclude that low-shade agroforestry provides the best available compromise between economic forces and ecological needs. Certification schemes for shade-grown crops may provide a market-based mechanism to slow down current intensification trends.agricultural economics ͉ agroforestry management ͉ land use change ͉ plant-animal interactions ͉ ecosystem goods and services G lobal-scale conversion of tropical rainforests and agricultural intensification are major causes of biodiversity loss, and threaten ecosystem functioning, sustainable land use and local economies depending on natural resources (1-3). Developing strategies to reconcile human needs with the integrity of our environment is a major task for ecologists and socio-economists alike (4), but multitaxa studies are rare (5-6) and too little is known about the human dimension of land use changes (4, 7-11) and consequences for ecosystem functioning (1,2,(12)(13)(14). Furthermore, most ecological and economic studies on ecosystem services are carried out separately so that information cannot be brought together (15). Particularly, quantitative data on potential tradeoffs between biodiversity loss and agricultural intensification including natural habitat conversion is missing. Two competing solutions propose either wildlife-friendly farming on the cost of agricultural yields or land sparing by agricultural intensification to minimize the demand for natural habitat (16). The evaluation of such opposing land use options depends on t...

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The second messenger cyclic di-adenosine monophosphate (c-di-AMP) is essential in the Gram-positive model organism and in related pathogenic bacteria. It controls the activity of the conserved riboswitch and of several proteins involved in potassium (K) uptake. We found that the YdaO protein was conserved among several different bacteria and provide evidence that YdaO functions as a K transporter. Thus, we renamed the gene and protein KimA (K importer A). Reporter activity assays indicated that expression beyond the c-di-AMP-responsive riboswitch of the upstream regulatory region occurred only in bacteria grown in medium containing low K concentrations. Furthermore, mass spectrometry analysis indicated that c-di-AMP accumulated in bacteria grown in the presence of high K concentrations but not in low concentrations. A bacterial strain lacking all genes encoding c-di-AMP-synthesizing enzymes was viable when grown in medium containing low K concentrations, but not at higher K concentrations unless it acquired suppressor mutations in the gene encoding the cation exporter NhaK. Thus, our results indicated that the control of potassium homeostasis is an essential function of c-di-AMP.

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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.

Natural forests in South-East Asia have been extensively converted into other land-use systems in the past decades and still show high deforestation rates. Historically, lowland forests have been converted into rubber forests, but more recently, the dominant conversion is into oil palm plantations. While it is expected that the large-scale conversion has strong effects on the carbon cycle, detailed studies quantifying carbon pools and total net primary production (NPPtotal ) in above- and belowground tree biomass in land-use systems replacing rainforest (incl. oil palm plantations) are rare so far. We measured above- and belowground carbon pools in tree biomass together with NPPtotal in natural old-growth forests, 'jungle rubber' agroforests under natural tree cover, and rubber and oil palm monocultures in Sumatra. In total, 32 stands (eight plot replicates per land-use system) were studied in two different regions. Total tree biomass in the natural forest (mean: 384 Mg ha(-1) ) was more than two times higher than in jungle rubber stands (147 Mg ha(-1) ) and>four times higher than in monoculture rubber and oil palm plantations (78 and 50 Mg ha(-1) ). NPPtotal was higher in the natural forest (24 Mg ha(-1)  yr(-1) ) than in the rubber systems (20 and 15 Mg ha(-1)  yr(-1) ), but was highest in the oil palm system (33 Mg ha(-1)  yr(-1) ) due to very high fruit production (15-20 Mg ha(-1)  yr(-1) ). NPPtotal was dominated in all systems by aboveground production, but belowground productivity was significantly higher in the natural forest and jungle rubber than in plantations. We conclude that conversion of natural lowland forest into different agricultural systems leads to a strong reduction not only in the biomass carbon pool (up to 166 Mg C ha(-1) ) but also in carbon sequestration as carbon residence time (i.e. biomass-C:NPP-C) was 3-10 times higher in the natural forest than in rubber and oil palm plantations.