Biological composition analysis of a natural medicine, Faeces Vespertilionis, with complex sources using DNA metabarcoding

Faeces Vespertilionis is a commonly used fecal traditional Chinese medicine. Traditionally, it is identified relying only on morphological characters. This poses a serious challenge to the composition analysis accuracy of this complex biological mixture. Thus, for quality control purposes, an accurate and effective method should be provided for taxonomic identification of Faeces Vespertilionis. In this study, 26 samples of Faeces Vespertilionis from ten provinces in China were tested using DNA metabarcoding. Seven operational taxonomic units (OTUs) were detected as belonging to bats. Among them, Hipposideros armiger (Hodgson, 1835) and Rhinolophus ferrumequinum (Schober and Grimmberger, 1997) were the main host sources of Faeces Vespertilionis samples, with average relative abundances of 59.3% and 24.1%, respectively. Biodiversity analysis showed that Diptera and Lepidoptera were the most frequently consumed insects. At the species level, 19 taxa were clearly identified. Overall, our study used DNA metabarcoding to analyze the biological composition of Faeces Vespertilionis, which provides a new idea for the quality control of this special traditional Chinese medicine.

Lime-Phosphorus Fertilizer Efficiently Reduces the Cd Content of Rice: Physicochemical Property and Biological Community Structure in Cd-Polluted Paddy Soil

Due to the biomagnifying effect in the food chains, heavy metals will cause serious harm to the food produced in paddy soil, and then threaten human health. The remediation of soil heavy metals by the addition of amendments is a common method. However, the combination of the two amendments has been less studied and its effect is unknown. In this study, we investigated the effects of different concentrations of a lime and calcium-magnesium phosphate (CMP) amendments metal availability and paddy soil bacteria biodiversity. The experiment proves that the addition of 0.5 and 1.0‰ amendment can effectively reduce cadmium (Cd) availability and the cadmium content in rice to be below 0.2 mg/kg, meeting the national food safety level. The results demonstrate that increasing pH and phosphorous (P) in soil were two important factors decreasing available cadmium. Furthermore, biodiversity analysis of the treated soil showed that the amendment increased biodiversity. Proteobacteria and Chloroflex were the most abundant bacteria at the phylum level, followed by Acidobacterium and Nitrospirae. The abundance of Bacterodietes-vadinHA17, Syntrophaceae, and Thiobacillus increased as phosphorous increased. Cadmium passivation might induce those species.

Influence of DNA extraction kits on the fungal DNA metabarcoding for freshwater environmental DNA

Background: Environmental DNA (eDNA) metabarcoding is a rapidly expanding technique for efficient biodiversity monitoring, especially of animals. Recently, the usefulness of aquatic eDNA in monitoring the diversity of both terrestrial and aquatic fungi has been suggested. In eDNA studies, different experimental factors, such as DNA extraction kits or methods, can affect the subsequent analyses and the results of DNA metabarcoding. However, few methodological studies have been carried out on eDNA of fungi, and little is known about how experimental procedures can affect the results of biodiversity analysis. In this study, we focused on the effect of the DNA extraction method on fungal DNA metabarcoding using freshwater samples obtained from rivers and lakes. Methods: DNA was extracted from freshwater samples using the DNeasy PowerSoil kit, which is mainly used to extract microbial DNA from soil, and the DNeasy Blood & Tissue kit, which is commonly used for eDNA studies on animals. We then compared PCR inhibition and fungal DNA metabarcoding results [i.e., operational taxonomic unit (OTU) number and composition] of the extracted samples. Results: No PCR inhibition was detected in any of the samples, and no significant differences in the number of OTUs and OTU compositions were detected between the samples processed using different kits. These results indicate that both DNA extraction kits may provide similar diversity results for the river and lake samples evaluated in this study. Therefore, it may be possible to evaluate the diversity of fungi using a unified experimental method, even with samples obtained for diversity studies on other taxa such as those of animals.

Diversity and Molecular Characterization of Endophytic fungi associated with Leaves of Acacianilotica

Fungal endophytesare colonized in different part of the plants and play important role in survival of plants in stressful habitat. In search of potential endophytic fungito produce bioactive metabolites inthis study we investigate thediversity of endophytic fungi associated with leaves of the Acacia nilotica plant. Twenty-six endophytic fungi were subjected to morphologicaland molecular identification with internal transcribes spacer (ITS) region sequenced. All 26 endophytic fungi were divided into nine genera Chaetomium, Amesia, Ovatospora, Penicillium, Phialemonium, Colletotrichum, Crinipellis, Acrophialophora, Cribbea. Most of them belonged to the phylum Ascomycota only one belonging to the phylum Basidiomycota. This study shows that Acacia leaves inhabitant by diverse group of endophytic fungi. The biodiversity analysis showed Chaetomium sp. Being dominant with the highest colonization frequency (26.9%). One of the Chaetomium sp. showed sequence similarity of93% with the species reported earlier, Further investigationsarein needed to harness the bioactive compounds.

DEVELOPMENT OF THE DATABASE «FOREST VEGETATION OF NORTHERN EURASIA» AT THE CENTER FOR FOREST ECOLOGY AND PRODUCTIVITY OF THE RUSSIAN ACADEMY OF SCIENCES

The formation of databases of digitized vegetation relevés and the publication of content about them promote cooperation between researchers in solving problems of biodiversity analysis, the exchange of the used data, and, thus, the increase in research representativeness. The article is devoted to the review of the origin and use of the database of relevés of forest vegetation and considers the tasks in which it is used. The current stage of work is characterized as follows: improvement of the database structure, features of the stored information, replenishment of the database, issues of administration, and cooperation organization. Based on the analysis of current trends in the vegetation science and taking into account the features of information stored in the database, the relevant scientific problems, for the solution of which the use of the database is promising, and technical tasks that need to be solved to ensure its continued use were formulated.

Author Correction: Passive eDNA collection enhances aquatic biodiversity analysis

A Correction to this paper has been published: https://doi.org/10.1038/s42003-021-01994-6

Passive eDNA collection enhances aquatic biodiversity analysis

Environmental DNA (eDNA) metabarcoding is a sensitive and widely used approach for species detection and biodiversity assessment. The most common eDNA collection method in aquatic systems is actively filtering water through a membrane, which is time consuming and requires specialized equipment. Ecological studies investigating species abundance or distribution often require more samples than can be practically collected with current filtration methods. Here we demonstrate how eDNA can be passively collected in both tropical and temperate marine systems by directly submerging filter membranes (positively charged nylon and non-charged cellulose ester) in the water column. Using a universal fish metabarcoding assay, we show that passive eDNA collection can detect fish as effectively as active eDNA filtration methods in temperate systems and can also provide similar estimates of total fish biodiversity. Furthermore, passive eDNA collection enables greater levels of biological sampling, which increases the range of ecological questions that eDNA metabarcoding can address.

KERAGAMAN DAN POTENSI PEMANFAATAN VEGETASI GULMA PASCA PERTANAMAN PADI DI DESA PENGGARON KECAMATAN MOJOWARNO KABUPATEN JOMBANG

A field study aims to determine the diversity and potential utilization of weed vegetation that grows after rice planting. This research was carried out in paddy fields after monoculture rice planting in Penggaron Village, Mojowarno District, Jombang Regency in July - September 2020. Sampling was based on the quadratic sampling method with sample plots arranged randomly. In each plot the data taken is the name, number and canopy (area of ​​cover) of each plant species to determine density, dominance and frequency. Data analysis includes vegetation analysis to determine Summed Dominance Ratio (SDR) and biodiversity analysis calculated using the Shannon - Wienner diversity index. The results of this study were 26 types of weed vegetation were found in post-rice planting land. The dominant vegetation types include Oryza sativa L .; Limnocharis flava (L.) Buchenav; Phyllanthus urinaria L .; Monochoria vaginalis (Burm.f.) pressl; and Cleome viscosa L with an SDR value of ≥ 5.30%. A total of 15 types of weeds have the potential to be used as a source of food, animal feed, and traditional medicine.