BIOTROPIA - The Southeast Asian Journal of Tropical Biology
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THE MINIMUM NUMBER OF VALVES FOR DIATOMS IDENTIFICATION IN RAWAPENING LAKE, CENTRAL JAVA
Get PDFTechnical challenges in using diatoms for paleolimnological studies include the identification and enumeration of diatom valves. The minimum number of valves required for identification varies, ranging from 100 to 700 valves of the dominant species. This task can be very time-consuming, particularly when diatom valves are scarce. This study was conducted to determine the minimum number of valves needed for identification in diatom assemblages from Rawapening Lake, Central Java, Indonesia. Based on 314 samples collected from Rawapening Lake, diatom counting efficiency exceeded 0.85 when a minimum of 300 valves was counted. The number of diatom species identified remained stable after counting at least 300 valves. Therefore, the minimum number of diatom valves required to represent the assemblage for paleolimnological analysis is 300
GENETIC DIVERSITY AND TRAIT ASSOCIATION ANALYSIS OF INDONESIAN RICE (Oryza sativa L.) GERMPLASM USING SSR MARKERS
Get PDFGenerating a new crop variety with certain desirable traits requires germplasm collection with wide genetic diversity to facilitate accelerated development of improved cultivars. This study was conducted to characterize genetic diversity of Indonesian rice accessions using SSR markers and their agro-morphological characters to allow the identification of Marker Trait Association (MTA). A survey of genetic diversity among 72 traditional landraces of 15 provinces in Indonesia and 24 improved varieties was conducted using four multiplex panels of 14 fluorescent-labeled SSR markers and 22 agro-morphological characters. A total of 140 alleles with an average of 10 alleles per locus and Polymorphism Information Content (PIC) values at 0.73. The population structure identified five subgroups. A total of 4 highly significant MTA were identified. One character with highly significant MTA was number of panicle associated with RM277. Based on SSR marker, RM105 had two MTAs for auricle color and ligule shape. After validation, these MTAs may be deployed to improve rice productivity
AN SNP MARKER POTENTIALLY LINKED TO SOMATIC EMBRYOGENESIS OF OIL PALM (Elaeis guineensis)
Get PDFOil palm (Elaeis guineensis) is one of the most important oil-bearing crops in the world. This crop can be vegetatively propagated only using tissue culture technique. Oil palm tissue culture technique has low efficiency, with callogenesis and embryogenesis stages as the limiting factors. Genetic factor has a major role in determining the success rate of these two stages. The use of molecular markers which represent the rate of embryogenesis or callogenesis has the potential to improve the efficiency of oil palm tissue culture process. In this study, SNP mining was conducted on embryogenesis transcriptome data, oil palm cDNA database, oil palm genome database, and oil palm SNP marker database in NCBI. The objective of this study was to obtain SNP marker which represents the embryogenesis potential, to be further used in marker-assisted selection of oil palm ortets. One SNP (EMB6) showed significant association with embryogenesis rate. This SNP was found in one of Auxin Response Factor (ARF) family genes. The nucleotide replacement from adenine to guanine changed the 307ⁿᵈ amino acid from isoleucine to methionine. Oil palms with adenine homozygote (A/A) pattern on EMB6 showed an 8-fold higher chance to produce significantly higher embryogenesis rate than adenine–guanine heterozygote (A/G)
HISTOLOGICAL ANALYSIS OF IN VITRO CULTURED COCONUT ENDOSPERM
No full textCoconut is an important plant for supporting the livelihood of people in tropical regions and is often regarded as a symbolic icon of the tropics. However, coconut fruits are large and heavy, posing a risk of injury when falling and hitting individuals standing beneath the tree. To prevent such accidents, ripe fruits must be harvested regularly. Coconut trees derived from in vitro–cultured endosperm are triploid and produce seedless fruits (without endocarp), which are significantly lighter and therefore safer. The objective of this study was to investigate plant regeneration from fresh and in vitro–cultured coconut endosperms. Both types of endosperm tissues were analyzed using histological methods. Solid endosperm from a seven-month-old post-anthesis coconut of the ‘Samoan Dwarf’ cultivar was collected and cultured in vitro using a modified Branton and Blake medium. Histological observations of fresh coconut endosperm revealed relatively uniform parenchyma cells in both size and shape, with nuclei containing one to five nucleoli. In contrast, three-month-old calli obtained from in vitro–grown endosperm in semi-solid medium displayed cells with diverse shapes and sizes, a high nucleus-to-cytoplasm ratio, and abundant starch, protein, and lipid deposits, indicating active cell division. Furthermore, seven-month-old calli grown in liquid medium contained embryogenic cells resembling proembryos. Fourteen-month-old bud-like structures developed in semi-solid medium showed clear histological features, including a meristematic layer, tunica–corpus organization, cortex-like region, and xylem tracheids. These findings indicate that the bud-like structure represents an early stage of shoot-bud formation in coconut endosperm. To our knowledge, this is the first report demonstrating early shoot-bud formation in coconut endosperm cultured in vitro
DISTRIBUTION OF INVASIVE PLANT SPECIES IN DIFFERENT LAND-USE SYSTEMS IN SUMATERA, INDONESIA
Get PDFDisturbances caused by the conversion of rain forests into agricultural systems provide an opportunity for the expansion of Invasive Plant Species (IPS). Bukit Duabelas National Park is one of the few remaining lowland forests in Jambi Province (Sumatera, Indonesia). The surrounding areas up to the national park borders have already been converted into jungle rubber agroforests as well as rubber and oil palm plantations which might lead to an increased spread of IPS into the forest. This study was aimed at compiling a list of IPS and determining their distribution and coverage of IPS in four land use systems (rain forest jungle rubber, rubber and oil palm plantations). Spatial distribution patterns were investigated by creating a horizontal vegetation profile diagram for the permanent plots of the EFForTS project (Ecological and Socioeconomic Functions of Tropical Lowland Rainforest Transformation Systems, http://www.uni-goettingen.de/crc990). The dominance of IPS was determined using Important Value Index. A total of forty IPS were identified across the four land-use systems. The numbers of IPS were the highest in oil palm (28 species) and rubber plantations (27 species), and the lowest in jungle rubber (10 species). IPS were absent in the lowland rain forest. The diversity of IPS was influenced by environmental factors, especially canopy openness. IPS with the highest ground coverage were Dicranopteris linearis and Clidemia hirta. Both of them were found in all three land-use systems outside the rain forest when the forest canopy opens due to illegal logging or other human disturbances. Therefore, reforestation of disturbed areas is recommended to prevent the spread of IPS
MODELING OF TREE GROWTH AFTER FOREST FIRE IN MOUNT CIREMAI NATIONAL PARK, INDONESIA
Get PDFForest fire is a massive threat to tropical forests, causing various negative impacts on nature and human beings. Forest fires often lead to alterations of forest structure and its functions. This study on tree growth after forest fire was conducted using a simulation model. The model was performed at the individual level of the plant community and built to analyze the potential for tree growth and scenarios for post-fire recovery. Five important tree species from the montane forest of Mount Ciremai were chosen to build the model based on four main parameters: plant growth rate, diameter at breast height (DBH), tree-to-grass competition, and tree-to-tree competition. The scenario for post-fire recovery was simulated by replanting similar species with 5 cm DBH seedlings. Predictions from our model showed that most of the chosen species would recover to their pre-fire condition after 37–50 years. Considering the limitations of competition after replanting, it is suggested to minimize tree-to-tree competition and apply silvicultural treatments to maximize tree growth and community recovery
ANTIBACTERIAL ACTIVITY OF RED PIGMENT ISOLATED FROM COASTAL ENDOPHYTIC FUNGI AGAINST MULTI-DRUG RESISTANT BACTERIA
Get PDFMultidrug-resistant (MDR) bacterial infections have become a serious problem for the last several decades. To solve this issue, the finding of new antibiotic candidates is an urgency. Natural pigment is known to have biological activity against pathogenic bacteria. Coastal fungi are an unexplored source of natural pigment to fight MDR bacteria. This research was aimed to isolate coastal endophytic fungi from smooth ant plant (Hydnophytum formicarum), to screen endophytic fungi that produce red pigment, to extract the red pigment, to determine antibacterial activity of the red pigment, and to identify the coastal endophytic fungi producing the red pigment. In this study, seven fungi were isolated as endophytic fungi from H. formicarum. There were three isolates that produced extracellular pigment, i.e., RS 1A produced red pigment, RS 3 produced black pigment, and RS 6A produced yellow pigment. Our study focused on the red pigment which was produced by endophytic fungus strain RS 1A. The yield of red pigment was 8.8657% (w/w). This study showed that red pigment had antibacterial activity against Escherichia coli, Acinetobacter baumannii, and Proteus mirabilis strain MDR. Based on molecular and morphological identification, the endophytic fungus strain RS 1A was identified as Aspergillus versicolor
OPTIMIZATION AND EFFICIENCY IMPROVEMENT OF IN-HOUSE IMMUNOAFFINITY COLUMN KU-AF02 FOR AFLATOXIN DETECTION
Get PDFIn-house immunoaffinity column for aflatoxins (AFs) detection is first developed by Kasetsart University since 2011, i.e. the first IAC prototype, KU-AF01. Detection of aflatoxin B (AFB) up to 200 ng is considered significantly efficient, but the production cost is considered high. The high cost was due to the cost of monoclonal antibody specific to aflatoxin and its supporting materials, i.e. CNBr-activated Sepharose 4B. Therefore, this study was aimed to improve the efficiency of in-house immunoaffinity columns by replacing CNBr-activated Sepharose 4B with other supporting materials and to lower the ratio of antibody to supporting materials. Response surface methodology (RSM) was applied to determine the optimum alternative supporting materials and the ratio. Results revealed that when compared with CNBr-activated Sepharose 4B, all materials tested could recover higher than 80% AFB, except the activated CH Sepharose 4B. Results also indicated that the optimum ratio was 0.4 mg anti-aflatoxin monoclonal antibody to 204 μL CNBr-activated Sepharose 4B. CNBr-activated Sepharose 4B was considered to provide the best precision in recovering AFB. KU-AF02 increased the ability to detect AFB to 500 ppb. The recovery of AFs in the reference materials using KU-AF02 was more than 96% successful, with HorRat value range of 0.34–0.76. The reference materials used were 2 levels of AFs in peanuts, i.e. 47.68 and 72.14 ng/g. In terms of quality control in IAC production, there were no significant differences among the 5 batches produced (p > 0.05). KU-AF02 demonstrated stable and constant percent recovery at 4°C for up to 12 months (tested with standard 200 ppb AFB). This study indicated that KU-AF02 could lower the ratio of supporting materials to the antibody and that KU-AF02 has high stability and has good ability for cleaning up AFs. Therefore, KU-AF02 is recommended to be used as an in-house immunoaffinity column for aflatoxin detection in Thailand
SEED GERMINATION OF Avicennia marina (Forsk.) Vierh. BY PERICARP REMOVAL TREATMENT
Get PDFAvicennia marina is one species used for building coastal ecosystem stabilization on the Surabaya shores because of its tolerance to high salinity levels and resistance to wave energy. Its existence is threatened by various factors, including land conversion, pollution, and the construction of inter-island bridges. The growth of A. marina is currently limited by seed dormancy. To increase propagation efficiency, seed viability and vigor were compared based on collection dates and pericarp removal methods. The results showed no relationship between the salinity levels of soaking water or seed buoyancy and seed viability or vigor. Collection dates may influence seed viability and vigor, as seeds collected in October and November germinated more quickly than those collected in December, although there were no differences in total germination. Hand-peeled seeds germinated more slowly than soaked seeds for all collection dates, but with no differences in total germination. Seeds collected in October and November grew more vigorously than those collected in December
SELECTION AND CHARACTERIZATION OF SIDEROPHORE-PRODUCING RHIZOBACTERIA AND POTENTIAL ANTAGONISTIC ACTIVITY TOWARD Ralstonia solanacearum
Get PDFRalstonia solanacearum is an important pathogen of tomato. An alternative method to control this disease is through the application of biocontrol agents. Plant Growth-Promoting Rhizobacteria (PGPR) can be used as potential biocontrol agents, and PGPR producing siderophores play an important role in disease suppression. This experiment was conducted to select and characterize siderophore-producing rhizobacteria from tomato and to determine their potential as antagonistic agents against R. solanacearum. Candidates of PGPR were isolated from tomato plants grown in West Java Province, Indonesia. The isolates were screened for siderophore production using CAS medium. Among the 29 siderophore-producing isolates that showed a negative hypersensitivity reaction, two isolates exhibited the widest inhibition zones against R. solanacearum. These isolates were CP1C and CP2D, with inhibition zone diameters of up to 3.6 mm and 7.0 mm, respectively. Based on 16S rDNA sequencing, isolate CP1C was identified as Brevundimonas sp., while isolate CP2D was identified as Enterobacter sp. Both isolates did not negatively affect plant height or plant dry weight when compared with the control