Profile of microbial community of organic and conventional rice field using metagenomic analysis

Organic farming can increase the diversity of soil bacterial. This research aimed to compare the profile of microbial community of organic and conventional rice fields in early (0 Day After Planting/DAP), mid (15 DAP), and late (45 DAP) fertilizer application period. The total DNA genome from the soil sample was extracted then analyzed metagenomically using Next Generation Sequencing (NGS). There was nine genus of bacteria found in high relative abundance, 95.28%, while 4.72% included in Domain of Archaea (genus Methanosaeta). Phylum of Firmicutes (genus Clostridium has 24.50% relative abundance, Bacillus 11.90%, Lactobacillus 9.69%); Proteobacteria (genus Defluviicoccus 12.10%, Buchnera 18.46%, Rosenbergiella 2.46%); and Actinobacteria (genus Nocardioides 12.21%, and Streptomyces 3.96%). Meanwhile, the average plant height of organic rice fields was shorter than conventional rice fields got directly measured coincided with soil sampled. Based on alpha and beta diversity analysis, the highest community diversity and abundance were found in organic rice field soil samples taken at 45 DAP, i.e., at the end of the fertilizer application period. However, in both organic and conventional rice field soils, there was almost no significant difference in the bacterial community, so it impacts that organic and conventional systems do not make a real difference in the total N, P available, CEC, and pH values. It makes a significant difference in organic C and organic matters.

Effect of Chlorella vulgaris extract on high sucrose diet-induced diabetes in Drosophila melanogaster

Microalgae Chlorella vulgaris is a microscopic green algae that has known potential as a source of food and medicine (functional food). However, the pharmacological capacity of this microalgae species against disease due to metabolic disorders is still not understood. Thus, this study aims to evaluate the effect of C. vulgaris extract on animal models of Drosophila melanogaster (Drosophila) which are fed high-sucrose diet (HSD). Wild type Drosophila was used in this study for 7 days of observation. Drosophila was divided into four groups consisting of the first group that was not treated as a control. The second group was treated with HSD (30%), the third group was treated with C. vulgaris extract (120 g/L) and the fourth group was treated with double treatment (HSD and C. vulgaris extract). The parameters observed included fecundity, hatchability, hemolymph glucose and triglyceride levels. The results showed that the extract of C. vulgaris was able to reduce the negative effects of giving HSD. The single treatment of C. vulgaris extract and double treatment between C. vulgaris extract and HSD significantly decreased levels of hemolymph glucose, triglycerides of Drosophila, while the parameters of fecundity and hatchability were significantly increased when compared to Drosophila which only received HSD treatment. The conclusion of this study is that C. vulgaris extract can be used as an antihyperglycemic agent which requires further study to prove the results that have been obtained.

Viability, productivity, and anatomical response of groundnuts (Arachis hypogaea L.) to biofertilizer-sludge biogas applications

Groundnuts (Arachis hypogaea L.) is one of the essential food commodities in Indonesia. The use of biofertilizer has been applied to various types of crops. Meanwhile, the effect of using biofertilizer-sludge biogas on groundnuts is yet unknown. This study aims to analyze the seed viability and vigour, yield productivity, the anatomical response of groundnuts, and optimum concentration that could increase the values of each parameter. Treatments given include applying biofertilizer-sludge with 15 levels of treatment concentration compared to groundnuts without biofertilizer-sludge application as a control. The land was divided into 16 beds for each treatment consisting of control, biofertilizer from 10, 15, 30 L/ha, sludge from 12, 24, to 36 ml, and variations dosage of biofertilizer and sludge combined. The parameters observed for viability and vigour include the percentage of seed germination (GP), seed vigor index (SVI) for yield, the value of harvest index (HI), dry weight of the harvest, and root-shoot ratio (R/S). Anatomical responses were observed with stem diameter, stem’s metaxylem diameter, root diameter, root’s metaxylem diameter, and seed diameter. The biofertilizer-sludge results significantly affected HI, R/S values, stem diameter, root’s metaxylem diameter, and seed diameter. This research concluded that the application of biofertilizer-sludge did not significantly affect the seed viability and vigour and the dry weight of the harvest. The application of biofertilizer-sludge in various doses of concentration resulted in a decrease in the stem metaxylem diameter and root diameter compared to the control. A total of 10 L/ha biofertilizer + 24 ml sludge was an optimum concentration to increasing HI and R/S values. For the increasing stem, root metaxylem, and seed diameter, biofertilizer 30 L/ha + sludge 12 ml, sludge 24 ml, and biofertilizer 15 L/ha + sludge 12 ml were the optimum concentrations, respectively.

Stability of watermelon phenotype characters (Citrullus lanatus (Thunb.) Matsum. & Nakai) from crossing ♀ ‘Putri Delima’ with ♂ ‘Maduri’

Watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai) is a horticultural plant that belongs to the Cucurbitaceae family with high public demand, however, local markets sometimes have limited supply. The existence of watermelon varieties that are not pest-resistant causes its production to be erratic. Therefore, plant breeding efforts are required to produce superior varieties through the stability test of plant characters. For watermelon to be certified as a new variety, it needs to possess a stable and adaptive character to various conditions. The F1 watermelon from crossing ♀ ‘Putri Delima’ with ♂ ‘Maduri’ produces inole-shaped fruit, red flesh, and a sweet taste. Therefore, this study aims to determine the stability of the phenotypic character of watermelon F2 from crossing ♀ ‘Maduri’ with cultivar ♂ ‘Putri Delima’ and was conducted in Jamusan, Bokoharjo, Prambanan, Sleman, D.I.Yogyakarta fields from August to December. There are five samples of ripe watermelons that were selected randomly while their phenotypic characters were observed qualitatively and quantitatively. Each F2 watermelon character was compared to F1, and the quantitative analysis was conducted using one-factor ANOVA with a confidence level of 5%. The results of quantitative character analysis between F2 and F1 showed a P (P-value)> 0.05. Meanwhile, the results of qualitative observations of F2 watermelon showed different flesh and skin color, while the harvest time from F1 was caused by the segregation of heterozygous crosses. Therefore, it is necessary to select superior phenotypic characters as desired for the next breeding.

Increasing the potential of Cajuput leaf waste as cattle feed through fermentation pretreatment

Waste of cajuput leaves (Melaleuca cajuputi Powell) has the potential to be used as an alternative cattle feed because it has a fairly high nutritional content. The nutritional content of cajuput leaf waste needs to be improved before being used as an alternative feed. The fermentation process can increase nutrient content in cajuput leaf waste and increase the digestibility of organic matter (OMD), dry matter digestibility (DMD), Ammonia (NH3), and Volatile Fatty Acid (VFA). This study aimed to determine the improvement of cajuput leaf waste nutrition with the help of yeast as well as the effect of fermented cajuput leaf waste along with a mixture of concentrates and field grass on digestibility, NH3, and VFA which were carried out in vitro test. The results showed the nutritional content of cajuput leaf waste fermented by yeast of Aspergillus chevalieri had the best value of protein 16.03%, fiber 16.92%, and fat 5.93%. The treatment R4 (50% cajuput leaf waste + 25% concentrate + 25% field grass) had the best digestibility (DMD=46.12%; DMO=32.08%), NH3 (8.37mM) and VFA (168.5mM) production.

ISSR based analysis of genetic variability of plantlets culture of pineapple (Ananas comosus L.) from Sipahutar, North Sumatera, Indonesia

Sipahutar pineapple is very popular in North Sumatra, because of the distinctive sweet taste and normal water content. Furthermore, it is large in size and has a yellow fruit skin color with greenish tips. However, the problem with Sipahutar pineapple production is the limited amount of good quality seeds. The utilization of in vitro culture techniques on pineapples allows the emergence of somaclonal variations, especially in plantlets that have undergone the subculture stage. This somaclonal variation is one of the problems in commercial seedling production, therefore, it is necessary to conduct an initial examination using the inter simple sequence repeat (ISSR) molecular marker. This study aimed to determine the genetic and primary stability of ISSR, which can be used in pineapple plants native to Sipahutar. The methods used include sample preparation, DNA isolation, primer optimization, ISSR primer amplification by PCR method, and electrophoresis. Furthermore, a total of 15 samples were amplified with six ISSR primers, and the data were analyzed by cluster method using the NTSYS-PC software. The final result was visualized in a dendrogram and analysis of diversity was conducted using GenAlex. The results showed that the level of genetic variability of the Sipahutar pineapple, which has undergone in vitro culture using six ISSR molecular markers was 76-97%. Meanwhile, the genetic variability level of the native to Sipahutar pineapple can be influenced by the long culture period and the use of N6-benzyladenine. The primers can be used to observe the genetic variability, except for ISSR 25 with a PIC value of 0.000.

Typification and taxonomic notes of Smilacaceae species in Java

Smilacaceae is known as a taxa with wide phenotypic variation and their taxonomical complexities remain unsolved. The three species of Smilacaceae housed in Java, are given nomenclature history. Since all the potential sources of original material have been investigated, but nothing has been identified, three neotypifications were designated here. Herbarium specimen of Koorders 34990β in Herbarium Bogoriense (BO) was chosen as the neotype of Smilax klotzschii. The de Groot & Wehlburg RD52 herbarium specimen in BO was chosen as the neotype of S. nageliana and Blume 463 herbarium specimen in L was chosen as the neotype of S. odoratissima.

Ex-situ conservation of the native orchid Coelogyne rochusseni de Vriese from the Bukit Rimbang and Bukit Baling Wildlife Reserve Areas

The native orchid Coelogyne rochussenii de Vriese is under threat of extinction, so conservation measures need to be taken. In-situ conservation is constrained by time, resources and costs, and the appropriate conservation must be ex-situ. Therefore, This study aims to determine the most effective method for ex-situ conservation, especially basal medium and activated charcoal, in order to determine the fastest germination. The method used in this research was a factorial completely randomized design, consisting of four different basal medium treatments, Knudson C, Vacin and Went, Murashige and Skoog, and Hyponex + Vitamin medium. This treatment was combined with the application of activated charcoal at 4 different levels, with concentrations of 0.1,2.3 g/L-1, the parameters observed were germination day (day), germination percentage (%), and percentage of contamination (%). The results of this study concluded that the conservation of the Native orchid Coelogyne Rochussenii de Vriese using various growing mediums and activated charcoal had a significant effect on the growth of the embryo culture native orchid. Hyponex + Vitamin medium with 3 g/L-1 is able to accelerate germination days to 29.33 days, increase germination percentage to 92.06%, and reduce contamination to 0%.

Morphological and molecular characters of Cherax quadricarinatus (von Martens, 1868) from Sermo Reservoir and Tambakboyo Retention Basin, Daerah Istimewa Yogyakarta, Indonesia

The Australian red claw freshwater crayfish, Cherax quadricarinatus is one of the most widely distributed and cultivated freshwater crayfish due to its high tolerance towards various environmental conditions. Native to North Australia and South Papua New Guinea, this crayfish was found in Tambakboyo Retention Basin in 2016 and Sermo Reservoir in 2019. This research was aimed to identify the morphological and molecular characters of C. quadricarinatus collected from Sermo Reservoir and Tambakboyo Retention Basin, Yogyakarta. The genetic information of the samples was compared to Australian red claw freshwater crayfish currently available. The methodology used for this research are morphological, morphometrical, meristic identification, and molecular identification using the PCR method. The primer used to be 1471 primers as the forward primer and 1472 primers as the reverse primer. In conclusion, all six specimens obtained were identified to be C. quadricarinatus. Morphological analysis using UPGMA showed that all specimens were formed one big cluster and has the highest similarity index (1.00). Molecular analysis using BLAST showed that specimen from Sermo Reservoir was 98.96% identical to C. quadricarinatus and specimen from Tambakboyo Retention Basin was 100% identical to C. quadricarinatus. Thus concluding that based on their morphological and molecular character, all samples of this study were C. quadricarinatus. This finding also contributes to the distribution information of C. quadricarinatus in Daerah Istimewa Yogyakarta

Identification endophytic fungi of Nutgrass (Cyperus rotundus L.) as solubilizing phosphate and indole-3-acetic acid producers

Low phosphate content in the soil can cause insufficient plant needs. Besides, the endophytic fungi of nutgrass have the potential as a phosphate solvent and can produce IAA (Indole-3-Acetic Acid). This study aimed to determine the levels of solubilizing phosphate and production of IAA (Indole-3-Acetic Acid) by the endophytic fungi of nutgrass and to identify the isolates based on rDNA-ITS sequences. The methods used were the isolation of endophytic fungi, analysis of solubilizing levels of phosphate and IAA production, and molecular analysis with rDNA-ITS sequences. Results of isolation and purification, found five isolates coded URT1, URT2, URT3, URT4, and URT5. The endophytic fungi of nutgrass were able to solubilizing phosphate levels around 54.03 - 87.83 ppm, with the highest levels produced by URT4 isolate. IAA levels around 5.58 - 45.50 ppm, with the highest levels produced by URT1 isolate. Based on molecular analysis with rDNA-ITS sequences, it showed that URT4 had 97.42% similarity to Aspergillus tereus species, while UTR1 had 100% similarity to Fusarium oxyporum species. To conclude, the endophytic fungi of nutgrass from A. tereus and F. oxyporum species have high levels of solubilizing phosphate and IAA production so that they are potential candidates for biofertilizer.