Salmonella infections across the globe are becoming more challenging to control due to the emergence of multidrug-resistant (MDR) strains. Lytic phages may be suitable alternatives for treating these multidrug-resistant Salmonella infections. Most Salmonella phages to date were collected from human-impacted environments. To further explore the Salmonella phage space, and to potentially identify phages with novel characteristics, we characterized Salmonella-specific phages isolated from the Penang National Park, a conserved rainforest. Four phages with a broad lytic spectrum (kills >5 Salmonella serovars) were further characterized; they have isometric heads and cone-shaped tails, and genomes of ~39,900 bp, encoding 49 CDSs. As the genomes share a <95% sequence similarity to known genomes, the phages were classified as a new species within the genus Kayfunavirus. Interestingly, the phages displayed obvious differences in their lytic spectrum and pH stability, despite having a high sequence similarity (~99% ANI). Subsequent analysis revealed that the phages differed in the nucleotide sequence in the tail spike proteins, tail tubular proteins, and portal proteins, suggesting that the SNPs were responsible for their differing phenotypes. Our findings highlight the diversity of novel Salmonella bacteriophages from rainforest regions, which can be explored as an antimicrobial agent against MDR-Salmonella strains.
Dryobalanops aromatica Gaertn. f. is a major tropical canopy species in lowland tropical rain forests in Peninsular Malaysia. Diurnal changes in net photosynthetic rate (A) and stomatal conductance to water vapor (g(s)) were measured in fully expanded young and old leaves in the uppermost canopy (35 m above ground). Maximum A was 12 and 10 micro mol m(-2) s(-1) in young and old leaves, respectively; however, because of large variation in A among leaves, mean maximum A in young and old leaves was only 6.6 and 5.5 micro mol m(-2) s(-1), respectively. Both g(s) and A declined in young leaves when T(leaf) exceeded 34 degrees C and leaf-to-air vapor pressure deficit (DeltaW) exceeded 0.025, whereas in old leaves, g(s) and A did not start to decline until T(leaf) and DeltaW exceeded 36 degrees C and 0.035, respectively. Under saturating light conditions, A was linearly related to g(s). The coefficient of variation (CV) for the difference between the CO(2) concentrations of ambient air and the leaf intercellular air space (C(a) - C(i)) was smaller than the CV for A or g(s), suggesting that maximum g(s) was mainly controlled by mesophyll assimilation (A/C(i)). Minimum C(i)/C(a) ratios were relatively high (0.72-0.73), indicating a small drought-induced stomatal limitation to A and non-conservative water use in the uppermost canopy leaves.
Distribution of tropical rainforests in Southeastern Asia has changed over geo-logical time scale, due to movement of tectonic plates and/or global climatic changes. Shorea parvifolia is one of the most common tropical lowland rainforest tree species in Southeastern Asia. To infer population structure and demographic history of S. parvifolia, as indicators of temporal changes in the distribution and extent of tropical rainforest in this region, we studied levels and patterns of nucleotide polymorphism in the following five nuclear gene regions: GapC, GBSSI, PgiC, SBE2, and SODH. Seven populations from peninsular Malaysia, Sumatra, and eastern Borneo were included in the analyses. STRUCTURE analysis revealed that the investigated populations are divided into two groups: Sumatra-Malay and Borneo. Furthermore, each group contained one admixed population. Under isolation with migration model, divergence of the two groups was estimated to occur between late Pliocene (2.6 MYA) and middle Pleistocene (0.7 MYA). The log-likelihood ratio tests of several demographic models strongly supported model with population expansion and low level of migration after divergence of the Sumatra-Malay and Borneo groups. The inferred demographic history of S. parvifolia suggested the presence of a scarcely forested land bridge on the Sunda Shelf during glacial periods in the Pleistocene and predominance of tropical lowland rainforest at least in Sumatra and eastern Borneo.
Cresol Red, a commercial dye that used widely to color nylon, wool, cotton, and polyacrylonitrile-modified nylon in the massive textile manufacture is toxic recalcitrant. Absidia spinosa M15, a novel fungal strain isolated from a tropical rain forest, was found to decolorize Cresol Red 65% within 30 d under agitation condition. UV-Vis spectroscopy, TLC analysis and mass spectra of samples after decolorization process in culture medium confirmed final decolorization of Cresol Red. Two metabolites were identified in the treated medium: benzeneacetic acid (tR 9.6 min and m/z 136) and benzoic acid (tR 5.7 min and m/z 122). Laccase showed the significant activity (133.8 U/L) in biomass obtained at the end of experiment demonstrates role of the enzyme in the decolorization process.
The responses of lowland tropical communities to climate change will critically influence global biodiversity but remain poorly understood. If species in these systems are unable to tolerate warming, the communities-currently the most diverse on Earth-may become depauperate ('biotic attrition'). In response to temperature changes, animals can adjust their distribution in space or their activity in time, but these two components of the niche are seldom considered together. We assessed the spatio-temporal niches of rainforest mammal species in Borneo across gradients in elevation and temperature. Most species are not predicted to experience changes in spatio-temporal niche availability, even under pessimistic warming scenarios. Responses to temperature are not predictable by phylogeny but do appear to be trait-based, being much more variable in smaller-bodied taxa. General circulation models and weather station data suggest unprecedentedly high midday temperatures later in the century; predicted responses to this warming among small-bodied species range from 9% losses to 6% gains in spatio-temporal niche availability, while larger species have close to 0% predicted change. Body mass may therefore be a key ecological trait influencing the identity of climate change winners and losers. Mammal species composition will probably change in some areas as temperatures rise, but full-scale biotic attrition this century appears unlikely.
Phyllopsora is a crustose to squamulose lichen genus inhabiting the bark of trees in moist tropical forests and rainforests. Species identification is generally challenging and is mainly based on ascospore morphology, thallus morphology and anatomy, vegetative dispersal units, and on secondary chemistry. While regional treatments of the genus have been conducted for Africa, South America and Australia, there exists no study focusing on the Asian and Melanesian species. Previously, 24 species of Phyllopsora s. str. have been reported from major national studies and checklists representing 13 countries. We have studied herbarium material of 625 Phyllopsora specimens from 18 countries using morphology, anatomy, secondary chemistry, and molecular data to investigate the diversity of Phyllopsora species in Asia and Melanesia. We report the occurrence of 28 species of Phyllopsora including the following three species described as new to science: P.sabahana from Malaysia, P.siamensis from Thailand and P.pseudocorallina from Asia and Africa. Eight species are reported as new to Asia. A key to the Asian and Melanesian species of Phyllopsora is provided.
The past 40 years in Southeast Asia have seen about 50% of lowland rainforests converted to oil palm and other plantations, and much of the remaining forest heavily logged. Little is known about how fragmentation influences recovery and whether climate change will hamper restoration. Here, we use repeat airborne LiDAR surveys spanning the hot and dry 2015-16 El Niño Southern Oscillation event to measure canopy height growth across 3,300 ha of regenerating tropical forests spanning a logging intensity gradient in Malaysian Borneo. We show that the drought led to increased leaf shedding and branch fall. Short forest, regenerating after heavy logging, continued to grow despite higher evaporative demand, except when it was located close to oil palm plantations. Edge effects from the plantations extended over 300 metres into the forests. Forest growth on hilltops and slopes was particularly impacted by the combination of fragmentation and drought, but even riparian forests located within 40 m of oil palm plantations lost canopy height during the drought. Our results suggest that small patches of logged forest within plantation landscapes will be slow to recover, particularly as ENSO events are becoming more frequent.
The therapeutic efficacy of the contemporary anti-inflammatory drugs are well established; however, prolonged use of such can often lead to serious and life-threatening side effects. Natural product-based anti-inflammatory compounds with superior efficacy and minimum toxicity can serve as possible therapeutic alternatives in this scenario. Genus Uvaria is a part of Annonaceae family, while the majority of its species are widely distributed in tropical rain forest regions of South East Asia. Uvaria species have been used extensively used as traditional medicine for treating all sorts of inflammatory diseases including catarrhal inflammation, rheumatism, acute allergic reactions, hemorrhoids, inflammatory liver disease and inflamed joints. Phytochemical analysis of Uvaria species has revealed flavones, flavonoids, tannins, saponins, polyoxygenated cyclohexene and phenolic compounds as major phyto-constituents. This review is an attempt to highlight the anti-inflammatory activity of Uvaria species by conducting a critical appraisal of the published literature. The ethnopharmacological relevance of Uvaria species in the light of toxicological studies is also discussed herein. An extensive and relevant literature on anti-inflammatory activity of Uvaria species was collected from available books, journals and electronic databases including PubMed, ScienceDirect, Scopus, Proquest and Ovid. Extracts and isolates of Uvaria species exhibited significant anti-inflammatory activity through various mechanisms of action. 6,7-di-O-Methyl-baicalein, flexuvarol B, chrysin, (-)-zeylenol, 6-hydroxy-5,7-dimethoxy-flavone, and pinocembrin were the most potent anti-inflammatory compounds with comparable IC50 with positive controls. Therefore, it is suggested that further research should be carried out to determine the pharmacokinetics, pharmacodynamics and toxicity of these therapeutically significant compounds, to convert the pre-clinical results into clinical data for drug development and design.
Tourism is associated with leisure and travelling, and is considered one of the fastest growing sectors that contribute significantly to the country’s economy, as well as bringing benefits directly to local communities. The Rural Tourism Master Plan was established in 2001, which defines rural tourism as an attraction that offers visitors the opportunity to experience Malaysia’s traditional culture and heritage away from urban areas. This study focuses on such tourism in the Gunung Mulu National Park, a famous natural park comprising underground caves, virgin rainforests and highlands. This research uses a quantitative approach with a random sampling technique because the procedure to select a unit for inclusion in a sample is much easier, quicker and cheaper. A questionnaire is distributed via Google Form to 500 local tourists who visited the park. The results of this research may be useful in marketing the Gunung Mulu National Park worldwide, besides fine-tuning programmes to attract tourists to the national park.
Black flies form a group of small blood-sucking insects of medical and veterinary importance. This study aimed to investigate the community structure, biodiversity and spatial and temporal distribution of adult black flies in tropical rain forests, by using malaise traps in Doi Inthanon National Park, northern Thailand. Malaise traps were placed along six elevational gradients (400 m to 2500 m, above sea level) at Doi Inthanon National Park, Chiang Mai province, from December 2013 to November 2014. A total of 9406 adult female black flies belonging to five subgenera-Daviesellum (2%), Gomphostilbia (23%), Montisimulium (11%), Nevermannia (16%) and Simulium (48%)-were collected. Among 44 taxa found, S. tenebrosum complex had the highest relative abundance (11.1%), followed by the S. asakoae species-group (9.6%), the S. striatum species-group (7.7%), S. inthanonense (6.6%), S. doipuiense complex (6.4%), S. chomthongense complex (5.3%), S. chumpornense (5.1%) and S. nigrogilvum (4.1%). Two human-biting species-S. nigrogilvum and species in the S. asakoae species-group-were found in all of the collection sites with 100% species occurrence. Species richness was highest at mid elevation (1400 m), which is represented by 19 black fly species. The peak and lowest seasonal abundance was observed in the rainy and hot season, respectively. Seasonal species richness was highest in the cold season, except for that from elevation sites at 700 m, 1700 m and 2500 m. This study revealed that the malaise trap is effective in providing important data for further monitoring of the effects of environmental changes and conservation planning on the biodiversity of black flies in Doi Inthanon National Park.
Malaysian Borneo has a lower population density and is an area known for its lush rainforests. However, changes in pollutant profiles are expected due to increasing urbanisation and commercial-industrial activities. This study aims to determine the variation of surface O3concentration recorded at seven selected stations in Malaysian Borneo. Hourly surface O3data covering the period 2002 to 2013, obtained from the Malaysian Department of Environment (DOE), were analysed using statistical methods. The results show that the concentrations of O3recorded in Malaysian Borneo during the study period were below the maximum Malaysian Air Quality Standard of 100ppbv. The hourly average and maximum O3concentrations of 31 and 92ppbv reported at Bintulu (S3) respectively were the highest among the O3concentrations recorded at the sampling stations. Further investigation on O3precursors show that sampling sites located near to local petrochemical industrial activities, such as Bintulu (S3) and Miri (S4), have higher NO2/NO ratios (between 3.21 and 5.67) compared to other stations. The normalised O3values recorded at all stations were higher during the weekend compared to weekdays (unlike its precursors) which suggests the influence of O3titration by NO during weekdays. The results also show that there are distinct seasonal variations in O3across Borneo. High surface O3concentrations were usually observed between August and September at all stations with the exception of station S7 on the east coast. Majority of the stations (except S1 and S6) have recorded increasing averaged maximum concentrations of surface O3over the analysed years. Increasing trends of NO2and decreasing trends of NO influence the yearly averaged maximum of O3especially at S3. This study also shows that variations of meteorological factors such as wind speed and direction, humidity and temperature influence the concentration of surface O3.
This study was carried out in Agricultural Park, Teluk Cempedak and Bukit Pelindung at Kuantan, Pahang in October 2007. These three areas were different in ecological characteristic, Agricultural Park is a lowland region in Kuantan rural area, Teluk Cempedak is Kuantan’s most famous beach, and Bukit Pelindung is a reserved rainforest which is 200 meters from the sea level. Fly specimens were collected using four different kinds of baits: dry prawn, salted fish, pork and mango. Each of these baits was placed in a plastic container and exposed for one hour to attract flies. Within 5 minutes, flies started swarming around the baits. The flies were more attracted to the pork and salted fish compared to the other two baits. Fifty one flies, one moth (Lepidoptera) and one wasp (Hymenoptera) were collected. In Agricultural Park, two Lucilia cuprina, one Chrysomya megacephala and one Sarcophaga sp. were collected. For Teluk Cempedak beach, there were two Sarcophagids, 31 Chrysomya megacephala, five Musca domestica, one Lucilia cuprina and one moth were caught. Flies collected from Bukit Pelindung included five C.megacephala, two Sarcophagids, one Musca domestica and one wasp. Most C.megacephala were attracted to the pork and salted fish.
This paper focuses on Langat River basin which is experiencing fast pace land use changes and accelerated soil erosion associated with land clearing and earthwork activities. Land use changes detected from Landsat imageries from 1989-1999 show that urban expansion is the most active, i.e. recording an expansion of 180% over that time period. The major land use reduction is the tropical dipterocarp rainforest located along the upper catchment of the Langat River and the mangrove forest found along Kuala Langat in the west. The 11% decline in the trend of the forest over that decade is anticipated to contribute in the near future. Results from logistic regression on the casual factors of rapid land use changes are attributed to three significant variables namely transport accessibility, population dynamics and agriculture. The eroded material due to land use changes enters into the Langat River systems as suspended sediments and contributed as non point source of pollution. Some finer sediment is being discharged offshore forming sediment plumes at the river estuary. Sediment plumes detected by Landsat TM imageries were analysed. It is found that the dispersion was not extensive and generally the suspended solids existed at low concentration (varying from 10-50 mg/l). This result is unexpected considering the rapid land use and land cover change that is occurring within the basins. These are mainly due to the loss of sediments during flooding into flood plain and active dredging of the river channels.
Dipterocarpaceae is the dominant tree family in the tropical rain forests of Southeast Asia. Borneo is the centre of diversity for the dipterocarps. Identification of hotspots is important for forest and biodiversity conservation efforts. Species Occurrence Models (SOMs) were generated for all 247 species of dipterocarps recorded in Sarawak using herbarium occurrence data and based on the best model selected. The species occurrence density map for each genus and category (endemic and non endemic) was generated by overlaying the SOMs of all species in each genus or category. The species occurrence density maps were analyzed with land cover map from Landsat 7-EMT+ images and protected forest areas for identifying hotspots for conservation in Sarawak. Overlaying the SOM maps revealed that areas in central Sarawak and the southwest region (northwest Borneo around Kuching) are the main hotspots of dipterocarp diversity in Sarawak while the coastal lowland areas in the lower Rejang and Baram River which are mainly peat swamp forest are poorer in species occurrence density. In terms of endemism, as with dipterocarp diversity, the mixed diptercarp forest of central Sarawak is also the most important hotspot. Gap analysis revealed that most protected forest areas are in southwest Sarawak (Bako, Kubah, Tanjung Datu and Gunung Gading National Parks) and in the northern part of Sarawak (Niah, Lambir Hills and Mt Mulu National Parks). This leaves the hotspot in the central part of Sarawak least protected. Protected areas only cover between 2 and 4% of the total areas for the different hotspots (75% species density) while majority of the hotspots that are still forested are outside the protected areas.
Copy number variations (CNVs) are genomic structural variations that result from the deletion or duplication of large genomic segments. The characterization of CNVs is largely underrepresented, particularly those of indigenous populations, such as the Orang Asli in Peninsular Malaysia. In the present study, we first characterized the genome-wide CNVs of four major native populations from Peninsular Malaysia, including the Malays and three Orang Asli populations; namely, Proto-Malay, Senoi, and Negrito (collectively called PM). We subsequently assessed the distribution of CNVs across the four populations. The resulting global CNV map revealed 3102 CNVs, with an average of more than 100 CNVs per individual. We identified genes harboring CNVs that are highly differentiated between PM and global populations, indicating that these genes are predominantly enriched in immune responses and defense functions, including APOBEC3A_B, beta-defensin genes, and CCL3L1, followed by other biological functions, such as drug and toxin metabolism and responses to radiation, suggesting some attributions between CNV variations and adaptations of the PM groups to the local environmental conditions of tropical rainforests.
Native species that forage in farmland may increase their local abundances thereby affecting adjacent ecosystems within their landscape. We used two decades of ecological data from a protected primary rainforest in Malaysia to illutrate how subsidies from neighboring oil palm plantations triggered powerful secondary 'cascading' effects on natural habitats located >1.3 km away. We found (i) oil palm fruit drove 100-fold increases in crop-raiding native wild boar (Sus scrofa), (ii) wild boar used thousands of understory plants to construct birthing nests in the pristine forest interior, and (iii) nest building caused a 62% decline in forest tree sapling density over the 24-year study period. The long-term, landscape-scale indirect effects from agriculture suggest its full ecological footprint may be larger in extent than is currently recognized. Cross-boundary subsidy cascades may be widespread in both terrestrial and marine ecosystems and present significant conservation challenges.
Managing tropical rain forests is difficult because few long-term field data on forest growth and the impact of harvesting disturbance are available. Growth models may provide a valuable tool for managers of tropical forests, particularly if applied to the extended forest areas of up to 100,000 ha that typically constitute the so-called forest management units (FMUs). We used a stand growth model in a geographic information system (GIS) environment to simulate tropical rain forest growth at the FMU level. We applied the process-based rain forest growth model Formix 3-Q to the 55,000 ha Deramakot Forest Reserve (DFR) in Sabah, Malaysia. The FMU was considered to be composed of single and independent small-scale stands differing in site conditions and forest structure. Field data, which were analyzed with a GIS, comprised a terrestrial forest inventory, site and soil analyses (water, nutrients, slope), the interpretation of aerial photographs of the present vegetation and topographic maps. Different stand types were determined based on a classification of site quality (three classes), slopes (four classes), and present forest structure (four strata). The effects of site quality on tree allometry (height-diameter curve, biomass allometry, leaf area) and growth (increment size) are incorporated into Formix 3-Q. We derived allometric relations and growth factors for different site conditions from the field data. Climax forest structure at the stand level was shown to depend strongly on site conditions. Simulated successional pattern and climax structure were compared with field observations. Based on the current management plan for the DFR, harvesting scenarios were simulated for stands on different sites. The effects of harvesting guidelines on forest structure and the implications for sustainable forest management at Deramakot were analyzed. Based on the stand types and GIS analysis, we also simulated undisturbed regeneration of the logged-over forest in the DFR at the FMU level. The simulations predict slow recovery rates, and regeneration times far exceeding 100 years.
Tropical rainforests are considered as hotspots for bird diversity, yet little is known about the system that upholds the coexistence of species. Differences in body size that are associated with foraging strategies and spatial distribution are believed to promote the coexistence of closely related species by reducing competition. However, the fact that many babbler species do not differ significantly in their morphology has challenged this view. We studied the foraging ecology of nine sympatric babbler species (i.e., Pellorneum capistratum, P. bicolor, P. malaccense, Malacopteron cinereum, M. magnum, Stachyris nigriceps, S. nigricollis, S. maculata, and Cyanoderma erythropterum) in the Krau Wildlife Reserve in Peninsular Malaysia. We investigated; i) how these babblers forage in the wild and use vegetation to obtain food, and ii) how these trophically similar species differ in spatial distribution and foraging tactics. Results indicated that most babblers foraged predominantly on aerial leaf litter and used gleaning manoeuvre in intermediate-density foliage but exhibited wide ranges of vertical strata usage, thus reducing interspecific competition. The principal component analysis indicated that two components, i.e., foraging height and substrate are important as mechanisms to allow the coexistence of sympatric babblers. The present findings revealed that these bird species have unique foraging niches that are distinct from each other, and this may apply to other insectivorous birds inhabiting tropical forests. This suggests that niche separation does occur among coexisting birds, thus following Gause' law of competitive exclusion, which states two species occupying the same niche will not stably coexist.
One obvious requirement for concerted action by a bacterial population is for an individual to be aware of and respond to the other individuals of the same species in order to form a response in unison. The term "quorum sensing" (QS) was coined to describe bacterial communication that is able to stimulate expression of a series of genes when the concentration of the signaling molecules has reached a threshold level. Here we report the isolation from aquatic environment of a bacterium that was later identified as Enterobacter sp.. Chromobacterium violaceum CV026 and Escherichia coli [pSB401] were used for preliminary screening of N-acyl homoserine lactone (AHL) production. The Enterobacter sp. isolated was shown to produce two types of AHLs as confirmed by analysis using high resolution tandem mass spectrometry. To the best of our knowledge, this is the first documentation of an Enterobacter sp. that produced both 3-oxo-C6-HSL and 3-oxo-C8-HSL as QS signaling molecules.
The vertical structure of a tropical rain forest is complex and multilayered, with strong variation of micro-environment with height up to the canopy. We investigated the relation between morphological traits of leaf surfaces and tree ecological characteristics in a Malaysian tropical rain forest. The shapes and densities of stomata and trichomes on the abaxial leaf surfaces and their relation with leaf characteristics such as leaf area and leaf mass per area (LMA) were studied in 136 tree species in 35 families with different growth forms in the tropical moist forest. Leaf physiological properties were also measured in 50 canopy and emergent species. Most tree species had flat type (40.4 %) or mound type (39.7 %) stomata. In addition, 84 species (61.76 %) in 22 families had trichomes, including those with glandular (17.65 %) and non-glandular trichomes (44.11 %). Most leaf characteristics significantly varied among the growth form types: species in canopy and emergent layers and canopy gap conditions had higher stomatal density, stomatal pore index (SPI), trichome density and LMA than species in understory and subcanopy layers, though the relation of phylogenetically independent contrasts to each characteristic was not statistically significant, except for leaf stomatal density, SPI and LMA. Intrinsic water use efficiency in canopy and emergent tree species with higher trichome densities was greater than in species with lower trichome densities. These results suggest that tree species in tropical rain forests adapt to a spatial difference in their growth forms, which are considerably affected by phylogenetic context, by having different stomatal and trichome shapes and/or densities.