Diversity and differentiation of <Emphasis Type="Italic">Oryza sativa</Emphasis> and <Emphasis Type="Italic">O. rufipogon</Emphasis> in Indonesia

Analysis of the genetic structure of Indonesian Oryza sativa and O. rufipogon using neighbour-joining trees based on single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers revealed that O. sativa in Indonesia is separated from O. rufipogon. Accessions of O. sativa in this study were differentiated into two major groups, indica and tropical japonica, excluding some varieties. SSR and SNP markers revealed the high value of differentiation (F _ST) and genetic distance (D) between indica and tropical japonica and we discovered four loci by SNP markers and one locus by SSR markers that play a role in differentiation between indica and tropical japonica. Interestingly, genetic diversity (H) in O. rufipogon was lower than that in O. sativa, however H in O. rufipogon was the highest and H in tropical japonica was the lowest when O. sativa was divided into two groups. Inbreeding coefficient (Fst) showed evidences that gene flow (Nm) between species and within species might be one of the mechanisms related to the diversification and differentiation of Indonesian rice germplasm by asymmetric pattern between species and within O. sativa as revealed by SSR and SNP markers. In addition, we found evidences on stabilizing selection in Indonesian rice germplasm and they might be the reasons why Indonesian rice germplasm did not differentiate due to source location of landrace. However, we found a weak relation between SSR and SNP markers probably due to highly polymorphic in SSR and the different properties of both markers.     

Soil pH Buffering Capacity and Nitrogen Availability Following Compost Application in a Tropical Acid Soil

Tropical acid soils are highly weathered as they exist under tropical environment with high rainfall and temperature throughout the year, which affects nitrogen availability. Soil organic nitrogen is important in estimating soil nitrogen availability. The combined use of urea and compost in this study was carried out to decrease sole dependence on urea, buffer soil acidification, and reduce nitrogen losses through leaching. Thus, soil buffering capacity, incubation, and organic nitrogen fractionation studies were conducted to determine soil buffering capacity, availability of total nitrogen, organic fractions nitrogen, and inorganic nitrogen in soil after 90 days of incubation following compost. Soil pH, buffering capacity, total nitrogen, organic nitrogen fractions, exchangeable ammonium, and available nitrate were higher in all treatments with compost and combined use of urea and compost. Total hydrolyzable nitrogen, ammonium-nitrogen, (ammonium + amino sugar)-nitrogen, amino sugar-nitrogen, and amino acid-nitrogen were higher in soils with urea and compost suggesting that decomposition of soil organic fractions nitrogen into inorganic nitrogen (ammonium and available nitrate was affected by the addition of urea and compost. Urea can be amended with compost to regulate availability nitrogen in soil for crop use.     

Minimizing Ammonia Volatilization from Urea in Waterlogged Condition Using Chicken Litter Biochar

Application of urea in lowland rice fields leads to ammonia (NH₃) volatilization and environmental pollution, and diminishes nitrogen recovery by rice (Oryza sativa L.). Amending urea with biochar could reduce NH₃ loss from urea as well as improve chemical properties of acid soils. An incubation study was conducted using a closed-dynamic air flow system to determine NH₃ volatilization from urea and chemical properties of an acid soil (Typic Paleudults). The soil was mixed with three rates of chicken litter biochar (20, 40, and 60 g pot^?1) and 1.31 g urea. Mixing an acid soil with biochar (60 g pot^?1) in waterlogged to stimulate conditions in paddy condition significantly reduced NH₃ loss and total titratable acidity. Biochar application also increased soil pH, total nitrogen, available nitrate, organic matter, total organic carbon, total carbon, available phosphorus, and exchangeable cations. Thus, chicken litter biochar can be used to reduce urea-N loss and ameliorate chemical properties of acid soils. This aspect is being embarked on in our on-going field experiments.     

Short Term Enhancement of Nutrients Availability in Zea mays L. Cultivation on an Acid Soil Using Compost and Clinoptilolite Zeolite

To avoid environmental pollution due to excessive use of inorganic fertilizers, it is essential to increase the availability of nutrients using environmentally friendly resources, such as composts and clinoptilolite zeolite, in soil fertility management. In this study, an attempt was made to use different rates of inorganic fertilizers, compost, and clinoptilolite zeolite to correct the ongoing excessive use of inorganic fertilizers. A pot study using maize (Zea mays L.) as a test crop was carried out to determine the effects of amending inorganic fertilizers with compost and clinoptilolite zeolite on: (i) selected soil chemical properties, and (ii) N, P, and K uptake and use efficiency in maize cultivation. The pot study was conducted for 45 days (tasseling stage of maize). Amending inorganic fertilizers with compost and clinoptilolite zeolite increased soil total N, exchangeable Ca, Mg, K, and available P. Furthermore, P and K uptake and use efficiency of maize were significantly improved upon amending inorganic fertilizers with compost and clinoptilolite zeolite. Soil chemical properties and productivity of maize on acid soils can be improved through co-application of compost and clinoptilolite zeolite. However, field application of the authors’ findings is being evaluated in an on-going field experiment.     

Traditional perennial crop-based agroforestry in West Java: the tradeoff between on-farm biodiversity and income

Agroforestry systems have been re-evaluated with a renewed scientific interest as appropriate models for achieving sustainable production while maintaining planned and associated biodiversity and agroecosystem functioning. Traditional bamboo-tree gardens in West Java are known to play substantial ecological and socioeconomic roles. In this study, we attempted to elucidate the relationship between income generation and biodiversity by studying 83 bamboo-tree gardens that varied in species composition and degree of commercialization. We conducted a survey of the vegetation and interviewed the owners or managers of each plot. We identified 42 planned and utilized species and 19 associated non-use species. Eight vegetation groups were identified by two-way indicator species analysis (TWINSPAN), each of which varied in individual densities of different utilization species types, Simpson’s diversity index, management intensities, and potential annual gross income. The group with the highest potential income generation was dominated by clove trees (Syzygium aromaticum); however, this group also had a lower level of diversity and higher levels of management intensity than the other groups, but all of the pairwise groups were not significantly different. About 60% of the villagers used at least some fuelwood as a domestic energy source, and almost all of them collected fuelwood from bamboo-tree gardens regardless of ownership. There were no significant differences in density of potential fuelwood species among the vegetation groups. There were significant positive correlations between income and most management activities. The regression model between gross income and Simpson’s diversity index with the best fit was a unimodal curve, which strongly suggests that maximum diversity can be conserved at an intermediate level of income. Nevertheless, this intermediate level of gross income is probably not adequate as the primary source of income for garden owners, although some gardens had the potential to achieve higher income levels with no decline in diversity. We suggest that maximizing individual density and multistratifying canopy layers could improve profitability within perennial crop-based agroforestry systems in West Java.     

Cold Plasma: A Potential Alternative for Rice Grain Postharvest Treatment Management in Malaysia

Use of pesticides, herbicides and fertilizers is among the techniques to control insect pests and fungal pathogens. However, the technique is the major contributor to severe environmental implications in terms of air, water and soil pollution. Besides, variable inconsistency becomes an important issue in the implementation of inclined bed dryers, leading to significant rice grain loss. Cold plasma technology has been widely proposed as a potential alternative for rice grain postharvest treatment management due to the presence of generated ionised gas that eventually produces reactive oxygen species or reactive nitrogen species. These species are used to decontaminate foodborne pathogens, mycotoxins and bacterial diseases. This review explores the current literature regarding cold plasma treatment technology, focusing on its efficiency as the microbial decontamination medium and insect pest mortality medium, and on the enhancement functional, nutritional and cooking properties, especially in rice grains. Previous studies have successfully demonstrated the ability of cold plasma treatment to significantly reduce the microbial count of foodborne pathogens, detoxify mycotoxins, and control seedborne rice seedling bacterial diseases. Previous studies have also proved that the implementation of cold plasma technology in postharvest management should be seriously considered for improving rice grain quantity and quality in Malaysia.     

Identification,pathogenicity and control of powdery mildew caused by Erysiphe elevata on Eucalyptus pellita in Sumatra,Indonesia

Powdery mildews are biotrophic ascomycetes that do not typically kill their hosts, but instead interfere with normal plant growth. In Indonesia, white powdery spots were observed forming on the upper part of fully developed leaves of Eucalyptus pellita planted in sand beds of a clonal nursery. Thus, this study aimed to identify the causal agent of eucalypt powdery mildew in Indonesia as well as to develop control strategies to better manage the disease. Pathogen identification was based on morphology, molecular characterization of DNA sequencing the ITS region and pathogenicity test. In addition, considering that some powdery mildews are inhibited by free moisture on leaves, efficacy of foliar watering was tested for disease control. Phylogenetic analyses showed that isolates collected from infected eucalypt plants grouped together with other sequences of the Erysiphe elevata clade with bootstrap support of 99%; a similar result was also confirmed by morphological observations. Pathogenicity of powdery mildew on eucalypt plants was confirmed through artificial inoculation, thus fulfilling the Koch's postulates. For disease control, foliar watering reduced the incidence of powdery mildew on mother plants. The reduction of the disease incidence began to be more evident at 2 weeks after trial establishment, and in the fourth week, the incidence was below 10% in all three treatments, while the control was above 20%. Therefore, we concluded that E. elevata is the causal agent of powdery mildew in Indonesia and that one application of foliar watering per week was enough to minimize the disease impact in the nursery.     

Design considerations of variable rate liquid fertilizer applicator for mature oil palm trees

Precision Agriculture - This research study focuses on the design of variable rate liquid fertilizer applicator which can measure the NPK status of soil and applies N, P and K nutrients...     

Effects of habitat type, vegetation structure, and proximity to forests on bird species richness in a forest–agricultural landscape of West Java, Indonesia

To halt biodiversity loss in the humid tropics of developing countries, it is crucial to understand the roles and effects of human-modified landscapes with fragmented forest remnants in maintaining biodiversity while fulfilling the demands of local communities and reducing poverty. To implement appropriate landscape planning for conserving biodiversity and ecosystem functioning, appropriate information is required about parameters of habitat suitability among various anthropogenic habitats with a range of distances to forests and vegetation characteristics, but such information is limited. We examined differences in avian communities between a remnant forest and four types of man-made forest (two mature plantations and two agroforests) in a forest–agricultural landscape of West Java, and we analyzed the effects of both local and landscape factors on various types of species richness in this landscape. The results from non-metric multidimensional scaling revealed avifauna in the two types of agroforest was clustered separately from that in the remnant forest, mainly because drastic declines in the abundance of forest specialists (including IUCN red-listed species) and their replacement with open-habitat generalists. The mixed-tree agroforests were colonized by 30 % of forest specialists and forest-edge species found in the remnant forest, and maintained the highest richness of species endemic to Indonesia among man-made forests, implying that some forest specialists and endemics might have adapted to ancient landscape heterogeneity. High proportion of insectivorous birds was found in the remnant forest (more than 50 %) and drastically decline in man-made forests, although the species richness of insectivores did not decline significantly in broad-leaved plantations. We concluded that protection of remnant forests should be prioritized to conserve forest bird diversity. However, as different environmental factors affected the richness values of different ecological groups, appropriate landscape design and habitat management could improve functional diversity in forest–agricultural landscapes in the tropics.