Malaysian Tropical Rain Forest Research Articles

Insights into the Quorum-Sensing Activity in Aeromonas hydrophila Strain M013 as Revealed by Whole-Genome Sequencing

Aeromonas hydrophila species can be found in warm climates and can survive in different environments. They possess the ability to communicate within their populations, which is known as quorum sensing. In this work, we present the draft genome sequence of A. hydrophila M013, a bacterium isolated from a Malaysian tropical rainforest waterfall.

Interaction of ectoparasites-small mammals in tropical rainforest of Malaysia

The literature regarding the diversity of ectoparasites and their interaction with their hosts remains largely inadequate in Malaysian tropical rainforest. We investigate the interaction patterns and specialization of ectoparasites infesting terrestrial small mammals (rodents and scandents) in Peninsular and Malaysian Borneo from samples made in 16 localities between 2008 and 2010. A total of 3,235 individuals of ectoparasites were collected during field surveys, resulting in an interaction network involving 47 ectoparasites that were distributed on 23 species of small mammals. The overall specialization index H2′ of all ectoparasites and host species was 0.67 which was considered moderate. Ticks appeared to be generalist with specialization index (H2′ = 0.35) while lice showed higher specialization (H2′ = 1) in selecting host species. The most diverse parasite assemblage was found on S. muelleri (Hs_w = 1.96). Specialization indices among ectoparasite species (dp) ranged from 0.03 to 1 while the indices among host species (dh) ranged from 0.20 to 1. Incomplete field data may have contributed to the high specialization indices. This study is significant as it can enhance our understanding the emergence and management of potential zoonotic diseases in Malaysia.

Discovery of Pantoea rodasii strain ND03 that produces N-(3-Oxo-hexanoyl)-L-homoserine lactone.

Proteobacteria use quorum sensing to regulate target gene expression in response to population density. Quorum sensing (QS) is achieved via so-called signalling molecules and the best-studied QS signalling system uses N-acyl homoserine lactones (AHLs). This study aimed to identify and characterize the production of AHLs by a bacterium ND03 isolated from a Malaysian tropical rainforest waterfall. Molecular identification showed that ND03 is a Pantoea sp. closely related to Pantoea rodasii. We used Chromobacterium violaceum CV026, an AHL biosensor for preliminary AHL production screening and then used high resolution triple quadrupole liquid chromatography-mass spectrometry, to confirm that P. rodasii strain ND03 produced N-(3-oxo-hexanoyl)-l-homoserine lactone (3-oxo-C6-HSL). To the best of our knowledge, this is the first report for such a discovery in P. rodasii strain ND03.

Spatial Scaling Effects on Soil Bacterial Communities in Malaysian Tropical Forests

Spatial scaling to some extent determines biodiversity patterns in larger organisms, but its role in microbial diversity patterns is much less understood. Some studies have shown that bacterial community similarity decreases with distance, whereas others do not support this. Here, we studied soil bacterial communities of tropical rainforest in Malaysia at two spatial scales: a local scale with samples spaced every 5 mover a 150-m transect, and a regional scale with samples 1 to 1,800 km apart. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1–V3 region was pyrosequenced using Roche/454 GS FLX Titanium platform. A ranked partial Mantel test showed a weak correlation between spatial distance and whole bacterial community dissimilarity, but only at the local scale. In contrast, environmental distance was highly correlated with community dissimilarity at both spatial scales,stressing the greater role of environmental variables rather than spatial distance in determining bacterial community variation at different spatial scales. Soil pH was the only environmental parameter that significantly explained the variance in bacterial community at the local scale, whereas total nitrogen and elevation were additional important factors at the regional scale.We obtained similar results at both scales when only the most abundant OTUs were analyzed. A variance partitioning analysis showed that environmental variables contributed more to bacterial community variation than spatial distance at both scales. In total, our results support a strong influence of the environment in determining bacterial community composition in the rainforests of Malaysia. However, it is possible that the remaining spatial distance effect is due to some of the myriad of other environmental factors which were not considered here, rather than dispersal limitation.

Bidirectional exchange of methyl halides between tropical plants and the atmosphere

AbstractUsing a stable isotope tracer technique, we studied the exchange of methyl chloride (CH3Cl) and methyl bromide (CH3Br) between plants and the atmosphere in a tropical rain forest in Malaysia. Most plant species examined showed not only production but also consumption of CH3Cl with a large net emission overall. In contrast, CH3Br consumption was comparable to its production, so the net emission was small. The rates of CH3Cl and CH3Br consumption were highly correlated with each other, and their ratio was consistent with reported values in terrestrial ecosystems, where microorganisms are responsible for the consumption. Such microorganisms might participate in the consumption we observed, as the consumption rates were faster in saplings, whose leaves were generally covered by epiphytic microorganisms, than in healthy looking leaves of mature trees.

Silica nanoparticles aid in structural leaf coloration in the Malaysian tropical rainforest understorey herb Mapania caudata.

Blue-green iridescence in the tropical rainforest understorey sedge Mapania caudata creates structural coloration in its leaves through a novel photonic mechanism. Known structures in plants producing iridescent blues consist of altered cellulose layering within cell walls and in special bodies, and thylakoid membranes in specialized plastids. This study was undertaken in order to determine the origin of leaf iridescence in this plant with particular attention to nano-scale components contributing to this coloration. Adaxial walls of leaf epidermal cells were characterized using high-pressure-frozen freeze-substituted specimens, which retain their native dimensions during observations using transmission and scanning microscopy, accompanied by energy-dispersive X-ray spectroscopy to identify the role of biogenic silica in wall-based iridescence. Biogenic silica was experimentally removed using aqueous Na2CO3 and optical properties were compared using spectral reflectance. Blue iridescence is produced in the adaxial epidermal cell wall, which contains helicoid lamellae. The blue iridescence from cell surfaces is left-circularly polarized. The position of the silica granules is entrained by the helicoid microfibrillar layers, and granules accumulate at a uniform position within the helicoids, contributing to the structure that produces the blue iridescence, as part of the unit cell responsible for 2 ° Bragg scatter. Removal of silica from the walls eliminated the blue colour. Addition of silica nanoparticles on existing cellulosic lamellae is a novel mechanism for adding structural colour in organisms.

Species associations among dipterocarp species co-occurring in a Malaysian tropical rain forest

Abstract:Spatial association patterns reflect underlying mechanisms of coexistence, community structure of plant species in tropical forests. We hypothesized that if spatial associations between two species shift toward segregation patterns during the course of growth, deterministic mechanisms, such as interspecific competition and habitat differentiation, would prevail, whereas if no directed change in spatial associations between two species is observed and, consequently, the initial association pattern is retained through growth, the two species would experience weak interspecific competition and show no habitat differentiation. To assess the underlying mechanisms operating between confamilial species, we analysed spatial associations among 11 dipterocarp species in terms of three growth stages distinguished on the basis of dbh in the Pasoh 50-ha plot in Peninsular Malaysia. We analysed the spatial associations of all possible combinations among identical stages (165 pairs) and among different stages (330 pairs) for each pair of 11 species, except between identical species. Our previous study revealed that the 11 species could be characterized into two classes: seven fast-growing species exhibited high growth and mortality rates, spatial aggregation on a small scale, and positive habitat associations, while four slow-growing species exhibited low growth and mortality rates, spatial aggregation on a large scale, and no habitat associations except one. Spatial segregation was observed between fast-growing species (32 pairs, 17%) and between species of different classes (35 pairs, 14%), but not between slow-growing species. Throughout the growth stages, positive associations with other species were maintained for slow-growing species versus fast-growing species. In contrast, changes in initial associations toward segregation were observed more in fast-growing species. These results indicated that interspecific competition or habitat differentiation dominated for fast-growing species, while non-directed random processes dominated for slow-growing species.

Wood density explains architectural differentiation across 145 co‐occurring tropical tree species

Summary1.Because of its mechanical properties, wood density may affect the way that trees expand their stem and crown to exploit favourable light conditions in a mechanically stable way. From engineering theory and wood density properties, it is predicted that in terms of biomass investment, low‐density wood is more efficient for vertical stem expansion, while high‐density wood is more efficient for horizontal branch expansion. So far, these predictions have rarely been tested by empirical studies.2.We tested these predictions for 145 co‐occurring tree species in a Malaysian tropical rainforest. For each species, we selected trees across a broad size range and measured architectural dimensions (stem diameter, height of the lowest foliage and crown width). We used a hierarchical Bayesian model to estimate species‐specific allometric relationships between architectural dimensions including estimated stem biomass. Then, we examined correlations between species wood density and estimated architectural variables at standardized heights.3.When species were compared at standardized tree heights, wood density correlated negatively with stem diameter and positively with stem biomass at most reference heights. This indicates that species with low wood density produce thicker stems but at lower biomass costs. Wood density correlated positively with crown width and negatively with height of the lowest foliage, which indicates that high wood density species have wider and deeper crowns than low wood density species. These relationships were maintained at most reference heights. However, the relationship with crown width was nonsignificant above 18 m height. This may reflect large plastic response of lateral crown expansion to a local condition.4. Wood density explains the trade‐off between effective vertical stem expansion and horizontal crown expansion across co‐occurring tropical tree species. Such mechanical constraints characterize the difference in tree architecture between low wood density species that show an efficient height expansion to attain better light conditions in the exposed canopy and high wood density species that show an efficient horizontal crown expansion to enhance current light interception and persistence in the shaded forest understorey. Our study thus suggests that the mechanical constraints set by wood density contribute to the co‐existence of species differing in architecture and light capture strategy.

Fluxes and concentrations of volatile organic compounds from a South-East Asian tropical rainforest

Abstract. As part of the OP3 field study of rainforest atmospheric chemistry, above-canopy fluxes of isoprene, monoterpenes and oxygenated volatile organic compounds were made by virtual disjunct eddy covariance from a South-East Asian tropical rainforest in Malaysia. Approximately 500 hours of flux data were collected over 48 days in April–May and June–July 2008. Isoprene was the dominant non-methane hydrocarbon emitted from the forest, accounting for 80% (as carbon) of the measured emission of reactive carbon fluxes. Total monoterpene emissions accounted for 18% of the measured reactive carbon flux. There was no evidence for nocturnal monoterpene emissions and during the day their flux rate was dependent on both light and temperature. The oxygenated compounds, including methanol, acetone and acetaldehyde, contributed less than 2% of the total measured reactive carbon flux. The sum of the VOC fluxes measured represents a 0.4% loss of daytime assimilated carbon by the canopy, but atmospheric chemistry box modelling suggests that most (90%) of this reactive carbon is returned back to the canopy by wet and dry deposition following chemical transformation. The emission rates of isoprene and monoterpenes, normalised to 30 °C and 1000 μmol m−2 s−1 PAR, were 1.6 mg m−2 h−1 and 0.46mg m−2 h−1 respectively, which was 4 and 1.8 times lower respectively than the default value for tropical forests in the widely-used MEGAN model of biogenic VOC emissions. This highlights the need for more direct canopy-scale flux measurements of VOCs from the world's tropical forests.

Insectivorous Birds and Environmental Factors Across an Edge-Interior Gradient in Tropical Rainforest of Malaysia

Insectivorous Birds and Environmental Factors Across an Edge-Interior Gradient in Tropical Rainforest of Malaysia

The structure of a food web in a tropical rain forest in Malaysia based on carbon and nitrogen stable isotope ratios

Abstract:Carbon and nitrogen stable isotope ratios (δ13C and δ15N) have been used to study the structure of food webs. However, few studies have examined how a terrestrial food web can be depicted by this technique. We measured δ13C and δ15N in various consumers of four trophic groups (detritivores, herbivores, omnivores and predators), including vertebrates and invertebrates (14 orders, ≥24 families), as well as canopy and understorey leaves in a tropical rain forest in Malaysia. We found that δ13C and δ15N of the consumers differed significantly among the trophic groups. The predators had significantly higher δ13C than the herbivores, and were similar in δ13C to the detritivores, suggesting that most predators examined depend largely on below-ground food webs. δ15N was higher in predators than detritivores by about 3‰. The comparison of δ13C in plant materials and herbivores suggests that most herbivores are dependent on C fixed in the canopy layers. The vertebrates had significantly higher δ15N and δ13C than the invertebrates of the same trophic group, likely reflecting differences in the physiological processes and/or feeding habits. This study indicates that stable isotope techniques can help better understanding of the terrestrial food webs in terms of both trophic level and the linkage of above- and below-ground systems.

Simulation of the vegetation structure and function in a Malaysian tropical rain forest using the individual-based dynamic vegetation model SEIB-DGVM

An individual-based Dynamic Global Vegetation Model, the SEIB-DGVM, was adapted to a Malaysian tropical rain forest by incorporating formulas and parameters from a gap dynamics model, FORMIX3. After calibration, the model reconstructed forest structure (i.e., size structure, leaf area index, and woody biomass) and carbon fluxes (i.e., gross and net primary productivity) of a dipterocarp forest in Pasoh, Peninsular Malaysia. Sensitivity analysis demonstrated that the model was robust; forest structure and ecosystem functions moderately fluctuated due to changes in parameters and climatic environments. Sensitivity analysis also indicated that the success and decay of a dominant species group that monopolized the canopy layer greatly affected those of a less abundant, shade-intolerant group. This result indicates that even if environmental changes do not exhibit clear effects on dominant canopy species and/or whole forest structure, such changes may still substantially impact the biodiversity of subdominant species. In simulations without gap formation, woody biomass was overestimated and a shade-intolerant species group was eliminated. This finding indicates that incorporating gap formation into the individual-based model is essential for the appropriate simulation of forest biomass and biodiversity in this Malaysian tropical rain forest.

Insectivorous Birds and Environmental Factors Across an Edge-Interior Gradient in Tropical Rainforest of Malaysia

The study objectives were to test: (1) the effects of the edge-interior gradient on under storey insectivorous bird abundance, density and diversity; (2) effects of environmental variables along an edge-interior gradient at population level (i.e., on each sub-guilds and species abundance); (3) possible effects of environmental structure along an edge-interior gradient at community level (i.e., species richness, diversity and total abundance). Fifteen hundred and four birds belonging to 49 species were recorded. Species composition differed along the edge-interior gradient at the guild and species level. The composition of insectivorous birds was correlated with the latter measured environmental variables. Based on bird-habitat associations along the edge-interior gradient, two groups were distinguished. Arboreal foliage gleaning insectivores were positively correlated with ground cover, light intensity, shrub cover and percent of shrub cover between 0.5 and 2 m high. While terrestrial insectivores, were sensitive to the forest edge and could indicate the quality of forest interior habitats associated with high humidity, dense canopy cover and deep litter depth. Forest remnants in the lowlands of Peninsular Malaysia that have a deep leaf litter layer, a dense canopy cover and high relative humidity are able to support insectivorous species that are sensitive to edge effects. As such these forests have important conservation value.

Growth strategies differentiate the spatial patterns of 11 dipterocarp species coexisting in a Malaysian tropical rain forest

We examined relationships between mortality rate, relative growth rate (RGR), and spatial patterns of three growth stages (small, medium, and large trees) for 11 dipterocarp species in the Pasoh 50-ha plot. Mortality rates for these species tended to be positively correlated with RGRs, although the correlation was significant only at the small-tree stage. Seven species with high growth and mortality rates exhibited peaks in spatial aggregation at small distances (<100 m) in small trees, but this aggregation disappeared in medium and large trees. In contrast, the other four species with low growth and mortality rates aggregated at large distances (>200 m) throughout the three growth stages in all but one species. Negative associations between different growth stages were observed only for the high-mortality species, suggesting density-dependent mortality. The high-mortality species showed habitat associations with topography, soil type, and the forest regeneration phase after gap formation, whereas the three low-mortality species only had associations with the forest regeneration phase. A randomization procedure revealed that these habitat associations explained little of their spatial aggregation. Our results suggest that the growth strategy has a large effect on the structuring of the spatial distribution of tree species through mortality processes.

LEAF HERBIVORY AND DECOMPOSABILITY IN A MALAYSIAN TROPICAL RAIN FOREST

There is accumulating evidence that similar suites of plant traits may affect leaf palatability and leaf litter decomposability. However, the possible association between leaf herbivory and litter decomposition rates across species in species-diverse natural ecosystems such as tropical rain forests remains unexplored, despite its importance in estimating the herbivory effects on carbon and nutrient cycling of ecosystems. We found no strong association between leaf herbivory and litter decomposition rates across 40 tree species in a Malaysian tropical rain forest, even though the leaf and litter traits were tightly correlated. This is because the leaf and litter traits related to herbivory and decomposition rates in the field were inconsistent. Leaf toughness accounted for only a small part of the variation in the herbivory rate, whereas a number of litter traits (the leaf mass per area, lignin to nitrogen ratio, and condensed tannin concentration) accurately predicted the decomposition rate across species. These results suggest that herbivory rate across species may not be strongly related to single leaf traits, probably because plant-herbivore interactions in tropical rain forests are highly diverse; on the other hand, plant-decomposer interactions are less specific and can be governed by litter chemicals. We also investigated two factors, phylogeny and tree functional types, that could affect the relationship between herbivory and decomposition across species. Phylogenetic relatedness among the species did not affect the relationship between herbivory and decomposition. In contrast, when the plants were segregated according to their leaf emergence pattern, we found a significant positive relationship between herbivory and decomposition rates for continuous-leafing species. In these species, the condensed tannin to N ratios in leaves and litter were related to herbivory and decomposition rates, respectively. However, we did not observe a similar trend for synchronous-leafing species. These results suggest that the relationship between herbivory and decomposition may be more greatly affected by functional types than by phylogenetic relatedness among species. In conclusion, our results suggest that well-defended leaves are not necessarily less decomposable litter in a tropical rain forest community, implying that herbivory may not generate positive feedback for carbon and nutrient cycling in this type of ecosystem.

Changes in photosynthesis and leaf characteristics with tree height in five dipterocarp species in a tropical rain forest

Variations in leaf photosynthetic, morphological and biochemical properties with increasing plant height from seedlings to emergent trees were investigated in five dipterocarp species in a Malaysian tropical rain forest. Canopy openness increased significantly with tree height. Photosynthetic properties, such as photosynthetic capacity at light saturation, light compensation point, maximum rate of carboxylation and maximum rate of photosynthetic electron transport, all increased significantly with tree height. Leaf morphological and biochemical traits, such as leaf mass per area, palisade layer thickness, nitrogen concentration per unit area, chlorophyll concentration per unit dry mass and chlorophyll to nitrogen ratio, also changed significantly with tree height. Leaf properties had simple and significant relationships with tree height, with few intra- and interspecies differences. Our results therefore suggest that the photosynthetic capacity of dipterocarp trees depends on tree height, and that the trees adapt to the light environment by adjusting their leaf morphological and biochemical properties. These results should aid in developing models that can accurately estimate carbon dioxide flux and biomass production in tropical rain forests.

How Baby Plants Avoid Getting Hurt and Blossom into Adulthood: The Story of a Tropical Seed

ABSTRACTThe seed shell of Mezzettia parviflora (Annonaceae), an understory tree from the lowland tropical rain forest of Malaysia, has an extraordinarily sophisticated structure. The shell is entirely made of sclerenchyma (mechanical support tissue) that is in all parts equally dense (about 95% of volume occupied by cell wall). Yet, differences in cell shape and orientation have a strong influence on fracture resistance. The structure appears designed to allow the seed to open for germination, but to limit predation by large animals.

Diversity and density of diurnal squirrels in a primary hill dipterocarp forest, Malaysia

Squirrels (Order Rodentia; Family Sciuridae) are among the group of small mammals that have high species diversity in the Malaysian tropical rain forests (Corbet &amp; Hill 1992). In Peninsular Malaysia alone a total of 14 diurnal and 11 nocturnal species has been recorded (Medway 1983). In Peninsular Malaysia, several studies on squirrels have been done which emphasized vertical stratification (Harrison 1962, Lim et al. 1977, MacKinnon 1978, Saiful et al. 2001a), diversity (Zubaid &amp; Ariffin 1997), home range sizes (Tamura 1993, Saiful et al. 2001b), social behaviour (Tamura &amp; Yong 1993) and impact of human disturbance on habitat (Johns 1987). These studies were conducted in lowland and hill forests that have been logged. There are, however, few studies on squirrel abundance in terms of their density in Peninsular Malaysia especially in primary ill forests. Therefore, the purpose of the present study is to provide baseline data and information on squirrel richness, diversity and abundance in the Malaysian primary hill forest.

Access to Soil Actinomycetes in Malaysian Tropical Rain Forests

Access to Soil Actinomycetes in Malaysian Tropical Rain Forests

Propelled balloons for harvesting and transporting timber

Studies of conventional tractor‐based systems in the tropical rainforest of Malaysia have provided convincing evidence that selective logging with acceptable levels of damage requires the exploitation of air‐borne systems. Following consideration of helicopter‐based systems as used in Malaysia and procedures involving both balloons and airships in America, a theoretical system based on propelled balloons carrying water as ballast is presented here. In this system, one unit would be used for delimbing standing trees, and another for transporting logs. Such a system could potentially generate a long‐term net revenue from the forest estimated at 3.5 times higher than that of a conventional tractor system.