A New Filter Based Cultivation Approach for Improving Aspergillus Identification using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS)

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) is widely used in clinical laboratories for routine identification of bacteria and yeasts. However, methodological difficulties are still apparent when applied to filamentous fungi. The liquid cultivation method recommended by Bruker Daltonics GmbH for identification of filamentous fungi by MALDI-TOF MS is labour intensive and time-consuming. In this study, growth of Aspergillus species on different (porous) surfaces was investigated with the aim to develop a more reliable, quicker and less laborious identification method using MALDI-TOF MS. Mycelial growth without sporulation mimicking liquid cultivation and reliable MALDI-TOF MS spectra were obtained when A. fumigatus strains were grown on and in between a polycarbonate membrane filter on Sabouraud dextrose agar. A database of in-house reference spectra was created by growing Aspergillus reference strains (mainly focusing on sections Fumigati and Flavi) under these selected conditions. A test set of 50 molecularly identified strains grown under different conditions was used to select the best growth condition for identification and to perform an initial validation of the in-house database. Based on these results, the cultivation method on top of a polycarbonate filter proved to be most successful for species identification. This method was therefore selected for the identification of two sets of clinical isolates that mainly consisted of Aspergilli (100 strains originating from Indonesia, 70 isolates from Qatar). The results showed that this cultivation method is reliable for identification of clinically relevant Aspergillus species, with 67% and 76% correct identification of strains from Indonesia and Qatar, respectively. In conclusion, cultivation of Aspergilli on top of a polycarbonate filter showed improved results compared to the liquid cultivation protocol recommended by Bruker in terms of percentage of correct identification, ease of MSP creation, time consumption, cost and labour intensity. This method can be reliably applied for identification of clinically important Aspergilli and has potential for identification of other filamentous fungi.

A three-dimensional (3D) printing approach to fabricate an isolation chip for high throughput in situ cultivation of environmental microbes

The 3D-printed iChip version made from thermoplastics or photopolymers can isolate microbial populations of a peat swamp in situ with a population profile different from that isolated via the standard in vitro Petri dish cultivation method.

The Bacterial Microbiome of the Tomato Fruit Is Highly Dependent on the Cultivation Approach and Correlates With Flavor Chemistry

The modes of interactions between plants and plant-associated microbiota are manifold, and secondary metabolites often play a central role in plant-microbe interactions. Abiotic and biotic (including both plant pathogens and endophytes) stress can affect the composition and concentration of secondary plant metabolites, and thus have an influence on chemical compounds that make up for the taste and aroma of fruit. While the role of microbiota in growth and health of plants is widely acknowledged, relatively little is known about the possible effect of microorganisms on the quality of fruit of plants they are colonizing. In this work, tomato (Solanum lycopersicum L.) plants of five different cultivars were grown in soil and in hydroponics to investigate the impact of the cultivation method on the flavor of fruit, and to assess whether variations in their chemical composition are attributable to shifts in bacterial microbiota. Ripe fruit were harvested and used for bacterial community analysis and for the analysis of tomato volatiles, sugars and acids, all contributing to flavor. Fruit grown in soil showed significantly higher sugar content, whereas tomatoes from plants under hydroponic conditions had significantly higher levels of organic acids. In contrast, aroma profiles of fruit were shaped by the tomato cultivars, rather than the cultivation method. In terms of bacterial communities, the cultivation method significantly defined the community composition in all cultivars, with the bacterial communities in hydroponic tomatoes being more variable that those in tomatoes grown in soil. Bacterial indicator species in soil-grown tomatoes correlated with higher concentrations of volatiles described to be perceived as “green” or “pungent.” A soil-grown specific reproducibly occurring ASV (amplicon sequence variants) classified as Bacillus detected solely in “Solarino” tomatoes, which were the sweetest among all cultivars, correlated with the amount of aroma-relevant volatiles as well as of fructose and glucose in the fruit. In contrast, indicator bacterial species in hydroponic-derived tomatoes correlated with aroma compounds with “sweet” and “floral” notes and showed negative correlations with glucose concentrations in fruit. Overall, our results point toward a microbiota-related accumulation of flavor and aroma compounds in tomato fruit, which is strongly dependent on the cultivation substrate and approach.

Response of Growth and Production of Red Ginger (Zingiber Officinale Rubrum Rosc.) to the Use of Compost as a Planting Media

Red ginger is a prima donna medicinal plant during this COVID-19 pandemic, because it can help the body's immunity. For this reason, a cultivation method that can increase production is needed. This study aims to see the effect of using compost on the production of red ginger plants. The study was conducted in April 2021 until it was completed. The results showed that the production of red ginger using oil palm empty fruit bunch compost media was higher than other compost media. Keywords: Production, Red Ginger, COVID-19.

Draft Genome Sequence of Cellulomonas sp. PS-H5, Isolated from Sekinchan Beach in Selangor, Malaysia

Cellulomonas sp. strain PS-H5 was isolated from Sekinchan Beach in Selangor, Malaysia, using an ex situ cultivation method. The present work reports a high-quality draft annotated genome sequence of this strain and suggests its potential glycoside hydrolase enzymes for cellulose, hemicellulose, and starch degradations.

Effect of Cultivation Methods on Seed Yield Traits, Oil Yield, and Fatty Acid Compositions of Cultivated Paeonia ostii

Paeonia ostii is recognized as an important oilseed tree peony species with potential as a raw material source for cosmetic and health care products, strong seed setting capacity, high seed oil yield, and abundant omega-3 polyunsaturated fatty acids. P. ostii, commonly called Fengdan, is widely cultivated in China. The cultivation method difference has an important influence on the oil-use feature, which is a key index for evaluating the quality of oilseed crops. This study aimed to select an optimal cultivation method to provide the first reference data for high-yield and high-quality seed oil harvesting and to facilitate the understanding of the quality difference in the formation mechanism of seed oil in cultivated P. ostii. This study selected five representative cultivation methods, open field cultivation, sunny slope cultivation, shady slope cultivation, understory intercropping cultivation, and high-altitude cultivation, and investigated the influence of cultivation method differences on the oil-use feature based on the three aspects of seed yield traits, oil yield, and fatty acid compositions. Six seed yield traits (fruit pod length, fruit pod width, fruit pod thickness, number of fruit pods per plant, 1000-grain weight, and seed yield per plant) and oil yield reached the maximum values of 7.75 cm, 6.99 cm, 1.57 cm, 11.33, 290.45 g, 85.8 g, and 30.41%, respectively, using the understory intercropping cultivation method. Fatty acid compositions were mainly identified as α-linolenic acid, linoleic acid, oleic acid, stearic acid, and palmitic acid, with significant content differences among different cultivation methods (P < 0.05). Functional component α-linolenic acid and total amounts of unsaturated fatty acids reached the maximum values of 46.85% and 65.23%, respectively, with high-altitude cultivation and understory intercropping cultivation. The seed yield traits, oil yield, and total amounts of unsaturated fatty acids were optimal with the understory intercropping cultivation method, whereas high-altitude cultivation was conducive to the accumulation of α-linolenic acid. Understory intercropping cultivation with appropriate altitude increases is recommended as a preponderant cultivation method for high-yield and high-quality seed oil harvesting for this crop.

The Sensitivity and Specificity of Loop-Mediated Isothermal Amplification and PCR Methods in Detection of Foodborne Mi-croorganisms: A Systematic Review and Meta-Analysis

Background: The loop-mediated isothermal amplification (LAMP) method is frequently used for identifying many microorganisms. The present review aimed to evaluate the sensitivity and specificity of LAMP method for detection of food-borne bacteria and to compare these features with those of polymerase chain reaction (PCR), as an alternative molecular diagnostic procedure, and with cultivation method, as the gold standard method. Methods: The literature was searched in electronic databases (PubMed, Scopus, Web of Science, and EMBASE) for recruiting publications within Jan 2000 to Jul 2021. We used the combinations of keywords including foodborne disease, LAMP, PCR, Loop-mediated isothermal amplification, and polymerase chain reaction. Meta-analysis was used to adjust the correlation and heterogeneity between the studies. The efficiency of the methods was presented by negative likelihood ratio, positive likelihood ratio, sensitivity, specificity, and odds ratio using forest plots. A P-value less than 0.05 was considered as statistical significance cut off. The confidence intervals were presented at the 95% interval. Results: Overall, 23 relevant studies were analyzed. The sensitivities of LAMP and PCR methods were estimated to be 96.6% (95% CI: 95.0-97.7) and 95.6% (95%CI: 91.5-97.8), respectively. The specificities of LAMP and PCR were also estimated to be 97.6% (95%CI: 92.6-99.3) and 98.7% (95%CI: 96.5-99.5), respectively. Conclusion: The specificities of LAMP and PCR assays were determined by comparing their results with cultivation method as the gold standard. Overall, the specificity of both PCR and LAMP methods was low for detection of fastidious bacteria. Nevertheless, LAMP and PCR methods have acceptable specificities and sensitivities, and their application in clinical practice necessitates more studies.

Evaluation of Turnip (Brassica rapa L.) Var PTWG for Yield and Relative Economics under Frontline Demonstrations in District Budgam

The study was conducted to evaluate the turnip variety purple top white globe for yield and yield contributing characters through front line demonstration in District Budgam for three consecutive years 2018,2019 and 2020.A total of 25 FLD’s were distributed in village Roshanabad of block Narbal, District Budgam. The results obtained reveals that the improved variety was having higher yield and hence better returns to the farmers as compared to the local variety. Study also revealed a wide gap in the production technology of turnip. The farmers themselves observed the difference between the improved variety and local. The yield increase of 57.9% over the control and B:C ratio of 3.48 in demonstration plot (2.13 in control) may be attributed to scientific cultivation method viz proper selection of variety, use of quality seed, seed treatment, proper spacing, recommended dose of fertilizers and integrated pest management.

The Use of Jayanti (Sesbania Sesban) Molluscicide in Overcoming Golden Snail, Pest Of Rice Plant in The Village of Bunut Baok, Central Lombok

As a result of the attack golden snails, rice production declined to 30 % in some places in the province of West Nusa Tenggara. Application of science and technology activities for the community ( IbM ) to address the problem of golden snail pest have been conducted in The Village of Bunut Baok, Central Lombok. IbM program conducted by subject matter covers characteristics of jayanti plant (Sesbania sesban ) and its cultivation method, characteristics of golden snail species that is pests of the rice plant, how to prepare and manufacture of jayanti molluscicide, and its application to control rice pest snails. The methods used include lecture, discussion, demonstration and practice. IbM activity followed by 12 members of Farmers Group Mohon Petunjuk Bunut Baok Village. The results of the practice is that the use of 1 ppm solution jayanti leaf can be lethal 48% to 84% of golden snail population. Other results achieved are covering the growing appreciation of farmers to plant jayanti, increasing farmers' knowledge and skills in identifying plants jayanti, skilled to make jayanti molluscicide, and its use to control rice pest golden snails.

PENGARUH KOMBINASI PUPUK ORGANIK DAN PUPUK HAYATI TERHADAP PERTUMBUHAN, PRODUKSI DAN MUTU PEGAGAN

<em>Gotu kola is one of the medicinal plants that has begun to be cultivated by the Indonesian people. It’s cultivation needs to follow the GAP to produce the qualified yield, including the use of fertilizers. Biofertilizers have been widely developed to reduce adverse effects of chemical fertilizers to the environment, thus an organic cultivation method can be an alternative. The aim of this study was to determine the effect of biofertilizer on growth and yield of gotu kola. This research was an experimental study with a completely randomized design (CRD) using 8</em> <em>planting media treatments consisting of (a) Soil + manure + dolomite; (b) Soil manure + 1 g biofertilizer; (c) Soil + dolomite + 1g biofertilizer; (d) Soil + manure + 3 biofertilizer; (e) Soil + dolomite + 3 biofertilizer; (f) Soil + manure + 5 g biofertilizer; (g) Soil + dolomite + 5 g biofertilizer; and (h) Soil + 3 g</em> <em>biofertilizer. Parameters observed were leaf area, stem length, number of leaves, number of tillers, fresh weight, dry weight and asiaticoside content. The results showed that combination treatment of biofertilizer (1 g) with dolomite (30 g) gives better effect in increasing the number of tillers and number of leaves, while the combination of biofertilizer (5 g) and dolomite (30 g) is the best for asiaticoside levels in gotu cola.</em>