Leaf venation networks of Bornean trees: images and hand-traced segmentations.

The data set contains images of leaf venation networks obtained from tree species in Malaysian Borneo. The data set contains 726 leaves from 295 species comprising 50 families, sampled from eight forest plots in Sabah. Image extents are approximately 1 × 1 cm, or 50 megapixels. All images contain a region of interest in which all veins have been hand traced. The complete data set includes over 30 billion pixels, of which more than 600 million have been validated by hand tracing. These images are suitable for morphological characterization of these species, as well as for training of machine-learning algorithms that segment biological networks from images. Data are made available under the Open Data Commons Attribution License. You are free to copy, distribute, and use the database; to produce works from the database; and to modify, transform, and build upon the database. You must attribute any public use of the database, or works produced from the database, in the manner specified in the license. For any use or redistribution of the database, or works produced from it, you must make clear to others the license of the database and keep intact any notices on the original database

Positive effects of ectomycorrhizal colonization on growth of seedlings of a tropical tree across a range of forest floor light conditions

In a shadehouse experiment we tested the effects of light, nutrients and ectomycorrhizal fungi (EMF) on the growth of Vatica albiramis van Slooten (Dipterocarpaceae) seedlings. We hypothesised that it is more advantageous for plants to form connections with EMF and to trade carbon for nutrients with EMF under high light than low light. The relationship between seedling growth and the proportion of ectomycorrhizal root tips was expected as positive in high light and as negative in low light. Light conditions simulated the forest understory (low; 3% full sunlight), a small gap (medium; 11%) and a large gap (high; 33%) and a fully factorial combination of nutrients (F−/+) and ectomycorrhizal colonization (EMF−/+) treatments were applied within light conditions. The application of EMF and nutrients did significantly alter seedling growth across the range of forest floor light conditions, however the key hypothesis was rejected as seedling growth under low light was not affected by increased EMF colonization of root tips (light:EMF colonization χ2 = 2.97, p = 0.23). In addition, the lack of difference in morphotype abundance across light conditions indicated that light changes may not favour the association to specific EMF in seedlings of this particular dipterocarp species. Our results suggest that antagonistic (non-beneficial to the plant) effects due to ectomycorrhizal colonization under a light constrained environment may not affect seedling growth of Vatica albirami

Influence of species functional strategy on leaf stoichiometric responses to fertilizer in a Bornean heath forest

The distribution of Bornean heath forest on white sand soils is believed to be due to element limitation and soil acidity. To determine the impact of both element limitation and soil acidity on tropical heath forest, we established a soil fertilization experiment to investigate the impact that increased soil N availability and reduced soil pH (using lime/CaCO3) had on a range of elements in tree leaves. We hypothesized that alterations in soil resource availability would cause changes in the tree leaf N:P ratio and concentrations of other elements and these changes would be influenced by species' functional strategies. The experiment was carried out in a Bornean heath forest on infertile soil over a 2-year period. We selected 10 common tree species, spanning acquisitive to conservative strategies and tested whether tree species functional strategies influenced tree leaf elemental concentrations after the fertilization. Leaf N:P ratios showed considerable differences among co-occurring species. Overall, we found that soil N addition treatments increased leaf N concentration, although leaf N:P ratios were not affected. Changes in leaf Al, Fe and S concentrations were correlated with species functional strategy: conservative species showed a greater increase in leaf Fe compared with acquisitive species, whereas acquisitive species showed a greater increase in leaf Al but a decrease in leaf S compared with conservative species. Synthesis. We show that soil elements uptake differs between acquisitive and conservative species and that acquisitive species may not take up soil elemental resources more effectively than conservative species. We suggest that the greater Fe acquisition by conservative species, in comparison to acquisitive species, might be due to a stress tolerance strategy. The overall increase in leaf N showed that, in this nutrient-poor forest, N is a fundamental requirement irrespective of species functional strategies. Given the increased leaf Al and Fe concentration after liming, we also suggest that these elements are important, and possibly limiting (Fe), in this heath forest

Diversity of mammalian species at natural licks in rain forest of Deramakot and their conservation

Natural licks are an important place for mammals to obtain mineral elements that are deficient in their diets. Although the tropical rain forests of Borneo are known for high mammalian diversity, little is known about the relationship between natural licks and mammals. To understand the use of natural licks by mammals and the role of natural licks to maintain the mammalian diversity and populations in Borneo, we conducted a field study in Deramakot Forest Reserve, Sabah. Twenty-nine species of mammals out of the 37 species known in the forests of Deramakot irrespective of food type were recorded on the natural licks. The mammals came to the natural licks to drink water rather than to eat soil. Analysis of the water from the natural licks showed that the concentrations of calcium, magnesium, potassium, and sodium as well as pH were significantly higher than those of the controls (stream and soil water). Foliar analysis of animal diets showed that potassium was significantly higher than sodium in concentration. This study indicated that the mammals might come for the ingestion of minerals, especially sodium, to maintain internal sodium/potassium balance. The natural licks are hot spots of mammalian diversity in Borneo because a cascade of food web (herbivores to carnivores) is formed

Physical conditions regulate the fungal to bacterial ratios of a tropical suspended soil

As a source of ‘suspended soils’, epiphytes contribute large amounts of organic matter to the canopy of tropical rain forests. Microbes associated with epiphytes are responsible for much of the nutrient cycling taking place in rain forest canopies. However, soils suspended far above the ground in living organisms differ from soil on the forest floor, and traditional predictors of soil microbial community composition and functioning (nutrient availability and the activity of soil organisms) are likely to be less important. We conducted an experiment in the rain forest biome at the Eden Project in Cornwall to explore how biotic and abiotic conditions determine microbial community composition and functioning in a suspended soil. To simulate their natural epiphytic lifestyle, 20 bird’s nest ferns (Asplenium nidus) were placed on a custom-built canopy platform suspended 8m above the ground. Ammonium nitrate and earthworm treatments were applied to ferns in a factorial design. Extracellular enzyme activity and Phospholipid Fatty Acid (PLFA) profiles were determined at zero, three and six months. We observed no significant differences in either enzyme activity or PLFA profiles between any of the treatments. Instead, we observed decreases in β-glucosidase and N-acetyl-glucosaminidase activity, and an increase in phenol oxidase activity across all treatments and controls. An increase in the relative abundance of fungi during the experiment meant that the microbial communities in the Eden Project ferns after six months were comparable with 20 ferns sampled from pristine tropical rain forest in Borneo

Comparing soil nitrous oxide and methane fluxes from oil palm plantations and adjacent riparian forests in Malaysian Borneo

Riparian forests are often kept as buffers between rivers and oil palm plantations. Many benefits of riparian forests, such as increasing biodiversity and providing a travel corridor for wildlife have been documented. Conversely, data on fluxes of the greenhouse gases nitrous oxide (N2O) and methane (CH4) from riparian forests are sparse. Nitrogen (N) from fertilizer applied in the oil palm plantations leached to the adjacent riparian forests, may increase emissions of N2O. Methane (CH4) fluxes might also differ between oil palm plantations and riparian forests due to carbon (C) availability. In this scoping study, we installed transects from three mature oil palm plantations to adjacent riparian forests within the SAFE project landscape in Sabah, Malaysia (https://www.safeproject.net) for measurements of greenhouse gases and associated parameters every 2 months for 13 months. Emissions of N2O were higher from riparian forests with 40.4 [95% confidence intervals (CI): 35.7–44.6] μg N2O-N m–2 h–1 than from an equivalent area of oil palm plantation 27.6 (CI: 23.1–32.3) μg N2O-N m–2 h–1. Methane uptake was significantly higher from the riparian forest with −14.7 (CI: −21.1 to −8.3) μg CH4-C m–2 h–1 compared to slight positive emission in the oil palm plantations of 6.3 (CI: 1.1–11.4) μg CH4-C m–2 h–1. We are contributing urgently needed flux data for less well studied riparian forests in the Tropics, however, additional long-term studies are needed to be able to draw wider conclusions than possible from this scoping study alone

Litter inputs, but not litter diversity, maintain soil processes in degraded tropical forests — a cross-continental comparison

Land-use change in tropical forests can reduce biodiversity and ecosystem carbon (C) storage, but although changes in aboveground biomass C in human-modified tropical forests are well-documented, patterns in the dynamics and storage of C belowground are less well characterised. To address this, we used a reciprocal litter transplant experiment to assess litter decomposition and soil respiration under distinct litter types in forested or converted habitats in Panama, Central America, and in Sabah, Malaysian Borneo. The converted habitats comprised a large clearing on the Panama Canal and oil palm plantation in Borneo; forested habitats comprised a 60-year old secondary forest in Panama and a disturbed forest in Borneo that was selectively logged until 2008. In each habitat, we installed mesocosms and litterbags with litter collected from old-growth forest, secondary forest or an introduced species: Elaeis guineensis in Borneo and Saccharum spontaneum in Panama. We measured litter mass loss, soil respiration, and soil microbial biomass during nine months at each site. Decomposition differed markedly between habitat types and between forest vs. introduced litter, but the decay rates and properties of old-growth and secondary forest litters in the forest habitats were remarkably similar, even across continents. Slower decomposition of all litter types in the converted habitats was largely explained by microclimate, but the faster decay of introduced litter was linked to lower lignin content compared to the forest litter. Despite marked differences in litter properties and decomposition, there was no effect of litter type on soil respiration or microbial biomass. However, regardless of location, litter type, and differences in soil characteristics, we measured a similar decline in microbial activity and biomass in the absence of litter inputs. Interestingly, whereas microbial biomass and soil respiration increased substantially in response to litter inputs in the forested habitats and the converted habitat in Panama, there was little or no corresponding increase in the converted habitat in Borneo, indicating that soil recovery capacity had declined substantially in oil palm plantations. Overall, our results suggest that litter inputs are essential to preserve key soil processes, but litter diversity may be less important, especially in highly disturbed habitats

Linking functional traits to multiscale statistics of leaf venation networks

Funding Information UK Natural Environment Research Council. Grant Number: NE/M019160/1 US National Science Foundation. Grant Number: DEB‐2025282 NERC Human‐modified Tropical Forest Programme. Grant Number: NE/M017508/1 Biodiversity And Land‐use Impacts on Tropical Ecosystem Function (BALI). Grant Numbers: NE/K016253/1, NE/K016253/1 Sime Darby Foundation Stability of Altered Forest Ecosystems (SAFE) Project Sabah Biodiversity Council Institute for Tropical Biology and Conservation (ITBC) at the University of Malaysia, Sabah (UMS) Sabah Forest Research Centre (FRC) at Sepilok Sabah Forestry Department SEARRP, Yayasan Sabah (Maliau Basin Conservation Area) Maliau Basin and Danum Valley Management Committees Acknowledgements Fieldwork was supported by Unding Jami, Matheus Henrique Nuñes, Rudi Saul Cruz Chino, Milenka Ximena Montoya, and South East Asia Rainforest Research Program (SEARRP) staff. Research was facilitated by Rob Ewers, Laura Kruitbos, Reuben Nilus, Glen Reynolds, and Charles Vairappan. Species identifications were made by Bernadus Bala Ola, Bill McDonald, Alexander Karolus, and MinSheng Khoo. This work also was supported by the UK Natural Environment Research Council (NERC; no. NE/M019160/1, to BB) and the US National Science Foundation (no. DEB‐2025282, to BB). This publication is a contribution from the NERC Human‐modified Tropical Forest Programme (no. NE/M017508/1, to YAT) and Biodiversity And Land‐use Impacts on Tropical Ecosystem Function (BALI) consortium (no. NE/K016253/1, to YM and no. NE/K016253/1, to YAT). The SAFE Project was funded by the Sime Darby Foundation and the UK NERC. The study areas are part of the Global Ecosystems Monitoring Network (GEM) via an ERC Advanced Investigator Award to YM (no. 321131). The project also was supported by the Stability of Altered Forest Ecosystems (SAFE) Project, the Sabah Biodiversity Council (SaBC, permits JKM/MBS.1000‐2/2 JLD.3‐126 and ‐154), the Institute for Tropical Biology and Conservation (ITBC) at the University of Malaysia, Sabah (UMS), the Sabah Forest Research Centre (FRC) at Sepilok, the Sabah Forestry Department, the SEARRP, Yayasan Sabah (Maliau Basin Conservation Area), and the Maliau Basin and Danum Valley Management Committees. Sean Gleason and several anonymous reviewers provided constructive feedback on the manuscript.Peer reviewedPublisher PD

Comparison of greenhouse gas fluxes from tropical forests and oil palm plantations on mineral soil

In Southeast Asia, oil palm (OP) plantations have largely replaced tropical forests. The impact of this shift in land use on greenhouse gas (GHG) fluxes remains highly uncertain, mainly due to a relatively small pool of available data. The aim of this study is to quantify differences of nitrous oxide (N2O) and methane (CH4) fluxes as well as soil carbon dioxide (CO2) respiration rates from logged forests, oil palm plantations of different ages, and an adjacent small riparian area. Nitrous oxide fluxes are the focus of this study, as these emissions are expected to increase significantly due to the nitrogen (N) fertilizer application in the plantations. This study was conducted in the SAFE (Stability of Altered Forest Ecosystems) landscape in Malaysian Borneo (Sabah) with measurements every 2 months over a 2-year period. GHG fluxes were measured by static chambers together with key soil physicochemical parameters and microbial biodiversity. At all sites, N2O fluxes were spatially and temporally highly variable. On average the largest fluxes (incl. 95 % CI) were measured from OP plantations (45.1 (24.0–78.5) µg m−2 h−1 N2O-N), slightly smaller fluxes from the riparian area (29.4 (2.8–84.7) µg m−2 h−1 N2O-N), and the smallest fluxes from logged forests (16.0 (4.0–36.3) µg m−2 h−1 N2O-N). Methane fluxes were generally small (mean ± SD): −2.6 ± 17.2 µg CH4-C m−2 h−1 for OP and 1.3 ± 12.6 µg CH4-C m−2 h−1 for riparian, with the range of measured CH4 fluxes being largest in logged forests (2.2 ± 48.3 µg CH4-C m−2 h−1). Soil respiration rates were larger from riparian areas (157.7 ± 106 mg m−2 h−1 CO2-C) and logged forests (137.4 ± 95 mg m−2 h−1 CO2-C) than OP plantations (93.3 ± 70 mg m−2 h−1 CO2-C) as a result of larger amounts of decomposing leaf litter. Microbial communities were distinctly different between the different land-use types and sites. Bacterial communities were linked to soil pH, and fungal and eukaryotic communities were linked to land use. Despite measuring a large number of environmental parameters, mixed models could only explain up to 17 % of the variance of measured fluxes for N2O, 3 % of CH4, and 25 % of soil respiration. Scaling up measured N2O fluxes to Sabah using land areas for forest and OP resulted in emissions increasing from 7.6 Mt (95 % confidence interval, −3.0–22.3 Mt) yr−1 in 1973 to 11.4 Mt (0.2–28.6 Mt) yr−1 in 2015 due to the increasing area of forest converted to OP plantations over the last ∼ 40 years