Effect of shade on biodiversity within coffee farms : a meta-analysis

Aligning crop production with conservation initiatives has long been a topic of debate, with agricultural intensification threatening biodiversity across the globe. Shade-grown coffee allows farmers to preserve biodiversity by providing viable habitat, but its conservation value remains unclear. In this meta-analysis, we screened existing literature using the PRISMA protocol to compare the effect of three shade intensities on species diversity and individual abundance: sun, low shade (LS) and high shade (HS). Furthermore, we examine differences between taxa, within taxa and between regions to establish which species benefit most from shade and whether these benefits vary dependent on geographical location. Out of 1889 studies, we included 69 studies in the analysis, and performed random-effects meta-analyses and meta-regressions. Overall, we found that species diversity was significantly higher in HS when compared to sun and LS, and species diversity in LS tended to be higher than in sun. In each treatment, the species diversity of birds was higher in the higher shade treatment, i.e., HS and LS. In addition, mammal and epiphyte species diversity was higher in HS when compared to LS. Similarly, studies from Latin America showed significantly higher species diversity and abundance in shaded farms when compared to sun farms. Studies conducted in Africa detailed the opposite relationship, with abundance being significantly higher in less shaded systems, highlighting that land-use strategies must be region-specific. Moving forward, strategies to conserve biodiversity within coffee farms should: 1) account for region-specific variables; 2) end further encroachment; 3) maintain connectivity; and 4) optimise yield through prioritising faunal and floral diversity

Agrochemicals and shade complexity affect soil quality in coffee home gardens

Soil quality can directly influence the health, yield, and quality of a particular crop species, and agrochemicals are often used to boost soil micro- and macro-nutrients. The excessive application of agrochemicals, however, is often the cause of imbalances in acidity and nutrient concentration and can cause soil to deteriorate. The presence of multiple shade trees in farmland can positively influence soil quality. Here, we evaluate the effect of agrochemical use (i.e., organic, mixed, and intensive) and shade tree complexity (i.e., sun, low, and high) on soil quality (i.e., pH, macronutrients, and micronutrients) in 56 coffee home gardens in Indonesia. We found that Al, Fe, K, and Mn were significantly higher in farms that used agrochemicals, and pH was more acidic in fields with intensive use of agrochemicals. C:N ratio and Mn were higher in soils with high shade complexity than in sun-exposed soils. The use of agrochemicals, however, is not sustainable as it increases the Al concentration and decreases pH, both of which are associated with poor coffee growth and reduced soil quality. Shade tree removal and the use of invasive, non-native species, such as eucalyptus, can also negatively influence soil quality, and thus the maintenance of complex shade cover with native trees should be prioritised

Does the presence of shade trees and distance to the forest affect detection rates of terrestrial vertebrates in coffee home gardens?

Complex agroforestry systems can host similar biodiversity levels to adjacent continuous forests and can offer important ecosystem services for wildlife. Species inhabiting adjacent forests, as well as species that prefer agroforestry systems, can benefit from this habitat matrix. It is necessary, however, to understand the species-specific adaptability to such a complex matrix. Indonesia is a biodiversity hotspot and hosts many endemic species that are threatened with extinction. Its human population relies heavily on agriculture, meaning that finding a balance between crop productivity and biodiversity is key for the long-term sustainability of local communities and wildlife. We aim to determine the influence of the presence of shade trees and distance to the forest on the detection rates of wildlife in coffee home gardens. In West Java, Indonesia, we monitored 23 gardens between April 2018 and March 2021 via camera traps, totalling 3856 days of monitoring in shade-grown and 3338 days in sun-exposed gardens. We also collected data in the nearby montane rainforest, totalling 1183 days of monitoring. We used Generalized Additive Models to estimate the influence of shade cover and distance to the forest on the detection rates of wildlife. The Sunda leopard cat Prionailurus javanensis was found more frequently in shade-grown gardens and used both the forest and agroforest matrix. Wild boars Sus scrofa mostly occurred in gardens adjacent to the forest, while barred buttonquails Turnix suscitator were associated with gardens far (>1 km) from the forest. Several species (civets Viverricula indica and Paradoxus musangus javanicus, Horsfield’s treeshrew Tupaia javanica, Javan ferret badger Melogale orientalis, Javan mongoose Herpestes javanicus) were not influenced by shade cover and distance to the forest, suggesting they are well adapted to the agroforestry system. Still, species of high conservation importance, such as Javan leopard Panthera pardus melas, Sunda porcupine Hystrix javanica, and grizzled langur Presbytis comata, were present in the forest but not in the agroforest, suggesting that the replacement of the forest by the agroforestry matrix is still detrimental. Nevertheless, it is important to maintain the complexity of the agroforestry system and connectivity with the neighbouring continuous forest to favour the long-term sustainability of this environment and the conservation of endemic species

Application of serum proteomics to the Women's Health Initiative conjugated equine estrogens trial reveals a multitude of effects relevant to clinical findings

Abstract Background The availability of serum collections from the Women's Health Initiative (WHI) conjugated equine estrogens (CEE) randomized controlled trial provides an opportunity to test the potential of in-depth quantitative proteomics to uncover changes in the serum proteome related to CEE and to assess their relevance to trial findings, including elevations in the risk of stroke and venous thromboembolism and a reduction in fractures. Methods Five independent large scale quantitative proteomics analyses were performed, each comparing a set of pooled serum samples collected from 10 subjects, 1 year following initiation of CEE at 0.625 mg/d, relative to their baseline pool. A subset of proteins that exhibited increased levels with CEE by quantitative proteomics was selected for validation studies. Results Of 611 proteins quantified based on differential stable isotope labeling, the levels of 116 (19%) were changed after 1 year of CEE (nominal P < 0.05), while 64 of these had estimated false discovery rates <0.05. Most of the changed proteins were not previously known to be affected by CEE and had relevance to processes that included coagulation, metabolism, osteogenesis, inflammation, and blood pressure maintenance. To validate quantitative proteomic data, 14 proteins were selected for ELISA. Findings for ten - IGF1, IGFBP4, IGFBP1, IGFBP2, F10, AHSG, GC, CP, MMP2, and PROZ - were confirmed in the initial set of 50 subjects and further validated in an independent set of 50 additional subjects who received CEE. Conclusions CEE affected a substantial fraction of the serum proteome, including proteins with relevance to findings from the WHI CEE trial related to cardiovascular disease and fracture. Clinical Trials Registration ClinicalTrials.gov identifier: NCT00000611http://deepblue.lib.umich.edu/bitstream/2027.42/112914/1/13073_2009_Article_113.pd

Fostering a wildlife-friendly program for sustainable coffee farming: The case of small-holder farmers in Indonesia

There is an urgent need for a global transition to sustainable and wildlife-friendly farming systems that provide social and economic equity and protect ecosystem services on which agriculture depends. Java is home to 60% of Indonesia’s population and harbors many endemic species; thus, managing agriculture alongside human well-being and biodiversity is vital. Within a community of ~400 coffee farmers in the province of West Java, we assessed the steps to develop a wildlife-friendly program until reaching certification between February 2019 and October 2020. We adopted an adaptive management approach that included developing common objectives through a process of stakeholder consultation and co-learning. We firstly investigated via interviews the expectations and the issues encountered by 25 farmers who converted to organic production in 2016. Their main expectations were an increase in income and an increase in coffee quality, while they had issues mainly in finding high quality fertilizers, reducing pests, and increasing productivity. We used this information to establish a problem-solving plan for the transition to community-wide wildlife-friendly practices. As part of the adaptive evaluation, we assessed the quality of coffee plantations before and after the implementation of coproduced actions. The quality of coffee significantly improved after our interventions to reduce the coffee berry borer, especially in the fields that started as inorganic and converted to organic. We uncovered additional issues to meet the standards for certification, including banning hunting and trapping activities and increasing coffee quality for international export. We describe the coproduced actions (agroforestry, conservation education, local law, organic alternatives) and phases of the program and discuss the potential barriers. We provide novel evidence of adaptive management framework successfully used to implement management actions and reach shared goals

The effectiveness of a biopesticide in the reduction of coffee berry borers in coffee plants

Context. Crop pest outbreaks are expected to become more frequent and unpredictable due to climate change, posing risks to ecosystem health and farmers’ livelihoods. At the same time, there is growing evidence that chemical pesticides can persist in the landscape and contribute to land degradation. The use of natural pesticides in place of chemical pesticides is hoped to manage pest outbreaks while also restoring pollinator populations and improving the quality of arable land. During the 1970s, many countries committed to promoting and legislating Integrated Pest Management (IPM) strategies (encouraging natural and holistic approaches to pest management), often including using natural pesticides, known as biopesticides. Objective. We assessed the effectiveness of a biopesticide on coffee berry borer (CBB; Hypothenemus hampei) presence in 57 small-holder coffee home gardens in West Java, Indonesia across three years. Methods. Prior to the application of the biopesticide, we randomly chose ten coffee plants from each field and recorded the proportion of healthy berries per plant (berries without pest infestation) as a control. In April 2020, we distributed the biopesticide in each of the 57 coffee home gardens and repeated the above experiment. The biopesticide was redistributed in October 2020 and April 2021. We repeated the experiment for the last time in April 2021. Results and conclusions. We found that CBB presence significantly decreased, with an inverse relationship between distance to natural forest and CBB presence and a positive relationship between shade cover and CBB presence. We also interviewed farmers in April 2021 to investigate their perception of the effectiveness of the biopesticide and 87% of farmers thought it was more effective than conventional pesticides. Significance. We contribute to the growing literature on the effectiveness of natural pesticides through assessing farmers’ perceptions of these methods and providing empirical evidence for their effectiveness in remedying CBB infestation. We hope that this study will empower farmers to make conscious land-use choices and provide government authorities with evidence to support increased accessibility to biopesticides

Novel proteins associated with risk for coronary heart disease or stroke among postmenopausal women identified by in-depth plasma proteome profiling

Background: Coronary heart disease (CHD) and stroke were key outcomes in the Women's Health Initiative (WHI) randomized trials of postmenopausal estrogen and estrogen plus progestin therapy. We recently reported a large number of changes in blood protein concentrations in the first year following randomization in these trials using an in-depth quantitative proteomics approach. However, even though many affected proteins are in pathways relevant to the observed clinical effects, the relationships of these proteins to CHD and stroke risk among postmenopausal women remains substantially unknown. Methods: The same in-depth proteomics platform was applied to plasma samples, obtained at enrollment in the WHI Observational Study, from 800 women who developed CHD and 800 women who developed stroke during cohort follow-up, and from 1-1 matched controls. A plasma pooling strategy, followed by extensive fractionation prior to mass spectrometry, was used to identify proteins related to disease incidence, and the overlap of these proteins with those affected by hormone therapy was examined. Replication studies, using enzyme-linked-immunosorbent assay (ELISA), were carried out in the WHI hormone therapy trial cohorts. Results: Case versus control concentration differences were suggested for 37 proteins (nominal $P$ < 0.05) for CHD, with three proteins, beta-2 microglobulin (B2M), alpha-1-acid glycoprotein 1 (ORM1), and insulin-like growth factor binding protein acid labile subunit (IGFALS) having a false discovery rate < 0.05. Corresponding numbers for stroke were 47 proteins with nominal $P$ < 0.05, three of which, apolipoprotein A-II precursor (APOA2), peptidyl-prolyl isomerase A (PPIA), and insulin-like growth factor binding protein 4 (IGFBP4), have a false discovery rate < 0.05. Other proteins involved in insulin-like growth factor signaling were also highly ranked. The associations of B2M with CHD ($P$ < 0.001) and IGFBP4 with stroke ($P$ = 0.005) were confirmed using ELISA in replication studies, and changes in these proteins following the initiation of hormone therapy use were shown to have potential to help explain hormone therapy effects on those diseases. Conclusions: In-depth proteomic discovery analysis of prediagnostic plasma samples identified B2M and IGFBP4 as risk markers for CHD and stroke respectively, and provided a number of candidate markers of disease risk and candidate mediators of hormone therapy effects on CHD and stroke. Clinical Trials Registration ClinicalTrials.gov identifier: NCT0000061

Flower visitation time and number of visitor species are reduced by the use of agrochemicals in coffee home gardens

Pollination services, from both wild and managed populations of insect pollinators, have degraded as a result of agricultural intensification. Whilst 75% of economically important crops depend on insect pollinators for cultivation, 40% of insect pollinator species are threatened with extinction. Pollination services must be preserved if there is to be enough food for a global population whose demand is expected to double, if not triple, by 2050. Pollinator diversity and pollinator efficiency have been found to increase as a result of wildlife-friendly farming practices (i.e., natural chemicals and fertilizers and agroforestry). We evaluated the presence of insect pollinators in 42 coffee home gardens in West Java, Indonesia. Via generalized linear mixed models, we found that number of visitor species (β = 0.418 ± SE 0.194, p = 0.031) and visitation time (β = 0.845 ± SE 0.308, p = 0.006) decreased as farms were more intensely managed, (i.e., used chemical pesticides), compared to fields using organic practices. As knowledge of pollination services is widespread amongst smallholder farmers in Indonesia and beyond due to the long-held tradition of beekeeping, these results will add to their existing knowledge and empower farmers to enhance resources for pollinator species through agroforestry and natural pest management. Although we found significant differences in pollination services provided in intensely managed and wildlife-friendly farms, chemical use can affect farms far beyond a particular area of production. Therefore, pollinator conservation must be applied at a landscape level and involve all stakeholders, including farmers, when making effective policies

Postmenopausal estrogen and progestin effects on the serum proteome

Background: Women's Health Initiative randomized trials of postmenopausal hormone therapy reported intervention effects on several clinical outcomes, with some important differences between estrogen alone and estrogen plus progestin. The biologic mechanisms underlying these effects, and these differences, have yet to be fully elucidated. Methods: Baseline serum samples were compared with samples drawn 1 year later for 50 women assigned to active hormone therapy in both the estrogen-plus-progestin and estrogen-alone randomized trials, by applying an in-depth proteomic discovery platform to serum pools from 10 women per pool. Results: In total, 378 proteins were quantified in two or more of the 10 pooled serum comparisons, by using strict identification criteria. Of these, 169 (44.7%) showed evidence (nominal P less than 0.05) of change in concentration between baseline and 1 year for one or both of estrogen-plus-progestin and estrogen-alone groups. Quantitative changes were highly correlated between the two hormone-therapy preparations. A total of 98 proteins had false discovery rates less than 0.05 for change with estrogen plus progestin, compared with 94 for estrogen alone. Of these, 84 had false discovery rates less than 0.05 for both preparations. The observed changes included multiple proteins relevant to coagulation, inflammation, immune response, metabolism, cell adhesion, growth factors, and osteogenesis. Evidence of differential changes also was noted between the hormone preparations, with the strongest evidence in growth factor and inflammation pathways. Conclusions: Serum proteomic analyses yielded a large number of proteins similarly affected by estrogen plus progestin and by estrogen alone and identified some proteins and pathways that appear to be differentially affected between the two hormone preparations; this may explain their distinct clinical effects