universal primers
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2023 ◽  
Vol 83 ◽  
Author(s):  
A. Belmok ◽  
T. Rodrigues-Oliveira ◽  
F.A.C. Lopes ◽  
R.H. Krüger ◽  
C.M. Kyaw

Abstract Polymerase chain reaction (PCR) assays targeting 16S rRNA genes followed by DNA sequencing are still important tools to characterize microbial communities present in environmental samples. However, despite the crescent number of deposited archaeal DNA sequences in databases, until now we do not have a clear picture of the effectiveness and specificity of the universal primers widely used to describe archaeal communities from different natural habitats. Therefore, in this study, we compared the phylogenetic profile obtained when Cerrado lake sediment DNA samples were submitted to 16S rDNA PCR employing three Archaea-specific primer sets commonly used. Our findings reveal that specificity of primers differed depending on the source of the analyzed DNA. Furthermore, archaeal communities revealed by each primer pair varied greatly, indicating that 16S rRNA gene primer choice affects the community profile obtained, with differences in both taxon detection and operational taxonomic unit (OTU) estimates.


2023 ◽  
Vol 83 ◽  
Author(s):  
S. P. M. Cotta ◽  
M. S. Marins ◽  
I.E. Marriel ◽  
U.G.P Lana ◽  
E.A. Gomes ◽  
...  

Abstract Organo-mineral fertilizers supplemented with biological additives are an alternative to chemical fertilizers. In this study, thermoresistant microorganisms from composting mass were isolated by two-step procedures. First, samples taken at different time points and temperatures (33 days at 52 ºC, 60 days at 63 ºC, and over 365 days at 26 ºC) were pre-incubated at 80 oC for 30 minutes. Second, the microbial selection by in vitro culture-based methods and heat shock at 60 oC and 100 oC for 2h and 4h. Forty-one isolates were able to grow at 60 °C for 4h; twenty-seven at 100 °C for 2h, and two at 100 °C for 4h. The molecular identification by partial sequencing of the 16S ribosomal gene using universal primers revealed that thirty-five isolates were from eight Bacillus species, one Brevibacillus borstelensis, three Streptomyces thermogriseus, and two fungi (Thermomyces lanuginosus and T. dupontii). Data from amylase, phytase, and cellulase activity assays and the enzymatic index (EI) showed that 38 of 41 thermo-resistant isolates produce at least one enzyme. For amylase activity, the highest EI value was observed in Bacillus licheniformis (isolate 21C2, EI= 4.11), followed by Brevibacillus borstelensis (isolate 6C2, EI= 3.66), Bacillus cereus (isolate 18C2, EI= 3.52), and Bacillus paralicheniformis (isolate 20C2, EI= 3.34). For phytase, the highest EI values were observed for Bacillus cereus (isolate 18C2, EI= 2.30) and Bacillus licheniformis (isolate 3C1, EI= 2.15). Concerning cellulose production, B. altitudinis (isolate 6C1) was the most efficient (EI= 6.40), followed by three Bacillus subtilis (isolates 9C1, 16C2, and 19C2) with EI values of 5.66, 5.84, and 5.88, respectively, and one B. pumilus (isolate 27C2, EI= 5.78). The selected microorganisms are potentially useful as a biological additive in organo-mineral fertilizers and other biotechnological processes.


BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Mei Jiang ◽  
Shu-Fei Xu ◽  
Tai-Shan Tang ◽  
Li Miao ◽  
Bao-Zheng Luo ◽  
...  

Abstract Background Bioassessment and biomonitoring of meat products are aimed at identifying and quantifying adulterants and contaminants, such as meat from unexpected sources and microbes. Several methods for determining the biological composition of mixed samples have been used, including metabarcoding, metagenomics and mitochondrial metagenomics. In this study, we aimed to develop a method based on next-generation DNA sequencing to estimate samples that might contain meat from 15 mammalian and avian species that are commonly related to meat bioassessment and biomonitoring. Results In this project, we found the meat composition from 15 species could not be identified with the metabarcoding approach because of the lack of universal primers or insufficient discrimination power. Consequently, we developed and evaluated a meat mitochondrial metagenomics (3MG) method. The 3MG method has four steps: (1) extraction of sequencing reads from mitochondrial genomes (mitogenomes); (2) assembly of mitogenomes; (3) mapping of mitochondrial reads to the assembled mitogenomes; and (4) biomass estimation based on the number of uniquely mapped reads. The method was implemented in a python script called 3MG. The analysis of simulated datasets showed that the method can determine contaminant composition at a proportion of 2% and the relative error was < 5%. To evaluate the performance of 3MG, we constructed and analysed mixed samples derived from 15 animal species in equal mass. Then, we constructed and analysed mixed samples derived from two animal species (pork and chicken) in different ratios. DNAs were extracted and used in constructing 21 libraries for next-generation sequencing. The analysis of the 15 species mix with the method showed the successful identification of 12 of the 15 (80%) animal species tested. The analysis of the mixed samples of the two species revealed correlation coefficients of 0.98 for pork and 0.98 for chicken between the number of uniquely mapped reads and the mass proportion. Conclusion To the best of our knowledge, this study is the first to demonstrate the potential of the non-targeted 3MG method as a tool for accurately estimating biomass in meat mix samples. The method has potential broad applications in meat product safety.


Plant Disease ◽  
2021 ◽  
Author(s):  
Huan Ren ◽  
Gao Yang ◽  
Xue Li ◽  
Shijun Xing ◽  
Yating Gao ◽  
...  

Citron (Citrus medica L.) is a perennial evergreen woody tree of Rutaceae family and Genus of Citrus. The citron is cultivated for its economic, medicinal and ornamental values in the south of China. (Yang et al., 2015). The shapes range from spherical to ovate and the sizes range from 3 to 5 kg (Klein et al., 2016). In June 2021, some postharvest citron fruits (Citrus medica var. medica) were found to have decay with a green or greyish mycelium on part or whole citron in 2 farmer’s markets in Kunming city, Yunnan Province (N 25°02′; E 102°42′), southwest China. Initial symptoms appeared as white, brown, and irregular necrotic spots in the pericarp. The lesions enlarged gradually and developed into green, water-soaked areas which extend rapidly. Eventually, the diseased fruits were rotten, soften, and the green spore masses confined to the surface (Fig. 1A). The incidence of this disease in postharvest citron fruits ranges from 15 % to 35 %, which is extremely destructive to the fruit of Rutaceae family plants (Chen et al., 2019). Small pieces (5 mm2) of symptomatic citron fruits were surface disinfected in 75 % ethanol and 0.3 % NaClO for 30 s and 2 min respectively, rinsed with distilled water for three times, blotted dry, placed onto potato dextrose agar (PDA) medium aseptically and incubated in a growth chamber at 25 ± 1 ℃, after 7 days, different colonies grew on PDA plates that were isolated and purified on new PDA medium at 25 ± 1 ℃ for 7 days. Inoculating repeatedly until six single-strain (XY01 to XY06) were obtained, and these isolates were stored in 15 % glycerol at –80 ℃ in a refrigerator in the State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan Agricultural University. The selected pathogens (XY01 to XY06) were inoculated on PDA medium, incubated at 25 ± 1 ℃. After 7 days, colonies of the isolate obverse are olive green, the white margin and greyish-green spores on the surface, and the reverse colorless to cream yellow or pale dull brown. Colonies texture was velutinous, with a special fragrance. The conidia structure was very fragile and break up easily into many cellular elements. Conidiophores were terverticillate, produced by subsurface or aerial hyphae, irregularly branched and composed of short stipes with few metulae and branches that terminate in whorls of three to six phialides, which are often solitary, cylindrical with a short neck. Conidia are hyaline to pale green, smooth-walled, without septate, partially ellipsoidal, or obovate (4.9 to11.9× 4.3 to 8.9 μm). Partial cylindrical (8.2 to 10.5× 2.7 to 5.3 μm), there are some small conidia, which were ellipsoidal or spherical (3.9 to 5.2× 2.7 to 5.2 μm). According to morphological characteristics, the fungus was identified as Penicillium digitatum (Pers.) Sacc. Isolate XY01 and XY02 were used for molecular identification and genomic DNA was extracted using the CTAB method (Aboul-Maaty & Oraby, 2019). The universal primers ITS1 and ITS4 were used to amplify and sequence the ITS1, 5.8S, and ITS2 rDNA region. Using NCBI’s BLASTn tools, the nucleotide sequences of XY01 and XY02 (Gen-Bank accessions MZ976843 and OK513274) show 100 % identity to MK450692 (P. digitatum strain CMV010G4). Pathogenicity tests have used the fruits (Citrus medica), which maturity was more than 80%. The pathogens (XY01, XY02) were cultured for 7 days on PDA medium, washed with sterilized water the resulting spore suspensions diluted to 1.0 × 106 spores/ml. Wounds (0.5 × 0.5 cm) were made on the surface of citron fruits by scraping with a sterile scalpel and then treated with 200 µl of spore suspension (Wild, 1994). Control citron fruits were treated with sterile water. citron fruits were incubated at 24-26 °C. Each treatment was performed in triplicate with 6 citron fruits. After 3 days, all fruits had developed lesions, in a water-stained, pale brown, and rapidly formed white hyphae, white mold layer was observed with a length of 1.5-2.5 cm and a width of 1-2 cm (Fig.1C), but control did induce infection. After 7 days, decay developed more quickly, the hyphae rapidly expanded on the surface of the pericarp, with vague and irregular edges, then a green mold layer was formed, the whole fruit was observed to rot and soften, When the citron was cut, the white flesh inside turned black and rotted (Fig.1B). P. digitatum was consistently reisolated from the inoculated plants but not from the controls. No symptoms developed on the control (Fig.1D). According to Koch’s postulates, the inoculated strains of XY01 and XY02 were the isolates causing citron decay disease. Based on symptoms, morphological characteristics, rDNA-ITS sequence analysis, and pathogenicity, this fungus was identified as P. digitatum. To our knowledge, this is the first report of the distribution of P. digitatum on Citron (Citrus medica) in China.


2021 ◽  
Vol 12 ◽  
Author(s):  
Yuxuan He ◽  
Likun Long ◽  
Wei Yan ◽  
Liming Dong ◽  
Wei Xia ◽  
...  

Microribonucleic acids (miRNAs) play significant roles in the regulation of biological processes and in responses to biotic or abiotic environmental stresses. Therefore, it is necessary to quantitatively detect miRNAs to understand these complicated biological regulation mechanisms. This study established an ultrasensitive and highly specific method for the quantitative detection of miRNAs using simple operations on the ground of the ligation reaction of ribonucleotide-modified deoxyribonucleic acid (DNA) probes. This method avoids the complex design of conventional reverse transcription. In the developed assay, the target miRNA miR156b was able to directly hybridize the two ribonucleotide-modified DNA probes, and amplification with universal primers was achieved following the ligation reaction. As a result, the target miRNA could be sensitively measured even at a detection limit as low as 0.0001 amol, and differences of only a single base could be detected between miR156 family members. Moreover, the proposed quantitative method demonstrated satisfactory results for overexpression-based genetically modified (GM) soybean. Ligation-based quantitative polymerase chain reaction (PCR) therefore has potential in investigating the biological functions of miRNAs, as well as in supervising activities regarding GM products or organisms.


2021 ◽  
Author(s):  
Sanni Hintikka ◽  
Jeanette E. L. Carlsson ◽  
Jens Carlsson

Environmental DNA (eDNA) metabarcoding from water samples has, in recent years, shown great promise for biodiversity monitoring. However, universal primers targeting the cytochrome oxidase I (COI) marker gene popular in metazoan studies have displayed high levels of nontarget amplification. To date, enrichment methods bypassing amplification have not been able to match the detection levels of conventional metabarcoding. This study evaluated the use of universal metabarcoding primers as capture probes to either isolate target DNA, or to remove nontarget DNA, prior to amplification by using biotinylated versions of universal metazoan and bacterial barcoding primers, namely metazoan COI and bacterial 16S. Additionally, each step of the protocol was assessed by amplifying both COI and bacterial 16S to investigate the effect on the metazoan and bacterial communities. Bacterial abundance increased in response to the captures (COI library), while the quality of the captured DNA was improved. The metazoan-based probe captured bacterial DNA in a range that was also amplifiable with the 16S primers, demonstrating the ability of universal capture probes to isolate larger fragments of DNA from eDNA. This concept could be applied to metazoan metabarcoding, by using a truly conserved site without a high-level taxonomic resolution as a target of capture, to isolate DNA spanning over a nearby barcoding region, which can then be processed through conventional metabarcoding by amplification protocol.


2021 ◽  
Vol 70 (2) ◽  
Author(s):  
Delia Palmira Gamarra Gamarra ◽  
Gilberto Torres Suarez ◽  
Charo Milagros Villar Quiñonez ◽  
Alistair R. McTaggart ◽  
Emerson Clovis Carrasco Lozano

Coffee leaf rust is the main disease that causes significant losses in Coffea arabica. In Peru, this disease caused epidemics between 2008 and 2013 with production losses of 35 %. The objective was to identify H. vastatrix using a morphological and molecular approach based on a phylogenetic species concept. Coffee leaf samples with symptoms of chlorotic lesions with the presence of yellow uredospores at different severity stages of different cultivars were collected from 11 locations in the departments of Pasco and Junin during 2017-2018. DNA was purified as proposed by Cristancho and coworkers. The major subunit of ribosomal DNA was amplified with universal primers LR0R and LR5, and sequenced by Macrogen and deposited in GenBank. Sequences from the genera Achrotelium, Blastospora, Cystopsora, Hemileia, and Mikronegeria were included for phylogenetic analysis. The results showed that the rust was distributed in coffee growing regions of Pasco: Villa Rica (Catimor, Caturra, and Gran Colombia); Oxapampa (Yellow Caturra), and Junín: San Luis de Shuaro (Catimor), Chanchamayo (Catimor), San Ramón (Catimor), Vitoc (Caturra), Pichanaki (Caturra), Río Negro (Caturra), Pangoa (Yellow Caturra, Gran Colombia, Limani). It was also grouped into a single clade with isolated H. vastatrix from Mexico and Australia, suggesting that they come from a common ancestor. This is the first confirmed report using molecular barcoding of H. vastatrix in the central jungle of Peru.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sonia Trujillo-Argueta ◽  
Rafael F. del Castillo ◽  
Daniel Tejero-Diez ◽  
Carlos Alberto Matias-Cervantes ◽  
Abril Velasco-Murguía

AbstractDNA barcoding can be useful for species identification and phylogenetic analysis, but its effectivity has not been verified in most neotropical cloud forest plants. We tested three plastid barcodes, rbcLa, matK, and trnH-psbA, in selected pteridophytes, a well-represented group in these forests, from a little-explored area in Oaxaca, Mexico, applying the CBOL criteria for barcoding. We used BLASTn, genetic distance, and monophyly tree-based analyses employing neighbor-joining (NJ), maximum likelihood (ML), and Bayesian inference methods. Universal primers for rbcLa and trnH-psbA were successfully amplified and bi-directionally sequenced, but matK could not be amplified for most species. rbcLa showed the highest species discrimination in BLASTn (66.67%). trnH-psbA exhibited higher significant interspecific divergence values than rbcL and rbcLa + trnH-psbA (two-sample sign test, P value < 2.2e−16). Using NJ and ML phylogenetic trees, monophyletic species were successfully resolved (100%), differing only in support values and displaying full agreement with the most recent fern classification. ML trees showed the highest mean support value (80.95%). trnH-psbA was the only barcode that could detect the Elaphoglossoideae subfamily. Species discrimination did not increase using rbcLa + trnH-psbA. rbcLa is useful for fern barcoding, trnH-psbA is most helpful for phylogenetic analyses, and matK may not work as a universal barcoding marker.


Plant Disease ◽  
2021 ◽  
Author(s):  
Yanxiang Qi ◽  
Yanping Fu ◽  
Jun Peng ◽  
Fanyun Zeng ◽  
Yanwei Wang ◽  
...  

Banana (Musa acuminate L.) is an important tropical fruit in China. During 2019-2020, a new leaf spot disease was observed on banana (M. acuminate L. AAA Cavendish, cv. Formosana) at two orchards of Chengmai county (19°48ʹ41.79″ N, 109°58ʹ44.95″ E), Hainan province, China. In total, the disease incidence was about 5% of banana trees (6 000 trees). The leaf spots occurred sporadically and were mostly confined to the leaf margin, and the percentage of the leaf area covered by lesions was less than 1%. Symptoms on the leaves were initially reddish brown spots that gradually expanded to ovoid-shaped lesions and eventually become necrotic, dry, and gray with a yellow halo. The conidia obtained from leaf lesions were brown, erect or curved, fusiform or elliptical, 3 to 4 septa with dimensions of 13.75 to 31.39 µm × 5.91 to 13.35 µm (avg. 22.39 × 8.83 µm). The cells of both ends were small and hyaline while the middle cells were larger and darker (Zhang et al. 2010). Morphological characteristics of the conidia matched the description of Curvularia geniculata (Tracy & Earle) Boedijn. To acquire the pathogen, tissue pieces (15 mm2) of symptomatic leaves were surface disinfected in 70% ethanol (10 s) and 0.8% NaClO (2 min), rinsed in sterile water three times, and transferred to potato dextrose agar (PDA) for three days at 28°C. Grayish green fungal colonies appeared, and then turned fluffy with grey and white aerial mycelium with age. Two representative isolates (CATAS-CG01 and CATAS-CG92) of single-spore cultures were selected for molecular identification. Genomic DNA was extracted from the two isolates, the internal transcribed spacer (ITS), large subunit ribosomal DNA (LSU rDNA), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), translation elongation factor 1-alpha (TEF1-α) and RNA polymerase II second largest subunit (RPB2) were amplified and sequenced with universal primers ITS1/ITS4, LROR/LR5, GPD1/GPD2, EF1-983F/EF1-2218R and 5F2/7cR, respectively (Huang et al. 2017; Raza et al. 2019). The sequences were deposited in GenBank (MW186196, MW186197, OK091651, OK721009 and OK491081 for CATAS-CG01; MZ734453, MZ734465, OK091652, OK721100 and OK642748 for CATAS-CG92, respectively). For phylogenetic analysis, MEGA7.0 (Kumar et al. 2016) was used to construct a Maximum Likelihood (ML) tree with 1 000 bootstrap replicates, based on a concatenation alignment of five gene sequences of the two isolates in this study as well as sequences of other Curvularia species obtained from GenBank. The cluster analysis revealed that isolates CATAS-CG01 and CATAS-CG92 were C. geniculata. Pathogenicity assays were conducted on 7-leaf-old banana seedlings. Two leaves from potted plants were stab inoculated by puncturing into 1-mm using a sterilized needle and placing 10 μl conidial suspension (2×106 conidia/ml) on the surface of wounded leaves and equal number of leaves were inoculated with sterile distilled water serving as control (three replicates). Inoculated plants were grown in the greenhouse (12 h/12 h light/dark, 28°C, 90% relative humidity). Necrotic lesions on inoculated leaves appeared seven days after inoculation, whereas control leaves remained healthy. The fungus was recovered from inoculated leaves, and its taxonomy was confirmed morphologically and molecularly, fulfilling Koch’s postulates. C. geniculata has been reported to cause leaf spot on banana in Jamaica (Meredith, 1963). To our knowledge, this is the first report of C. geniculata on banana in China.


PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0260105
Author(s):  
Arash Kheirodin ◽  
Mohammad Sayari ◽  
Jason M. Schmidt

Polyphagous pests cause significant economic loss worldwide through feeding damage on various cash crops. However, their diets in agricultural landscapes remain largely unexplored. Pest dietary evaluation in agricultural fields is a challenging task currently approached through visual observation of plant feeding and microscopic identification of semi-digested plant material in pest’s guts. While molecular gut content analysis using metabarcoding approaches using universal primers (e.g., rbcl and trnL) have been successful in evaluating polyphagous pest diet, this method is relatively costly and time-consuming. Hence, there is a need for a rapid, specific, sensitive, and cost-effective method to screen for crops in the gut of pests. This is the first study to develop plant-specific primers that target various regions of their genomes, designed using a whole plant genome sequence. We selected Verticillium wilt disease resistance protein (VE-1) and pathogenesis related protein-coding genes 1–5 (PR-1-5) as our targets and designed species-specific primers for 14 important crops in the agroecosystems. Using amplicon sizes ranging from 115 to 407 bp, we developed two multiplex primer mixes that can separate nine and five plant species per PCR reaction, respectively. These two designed primer mixes provide a rapid, sensitive and specific route for polyphagous pest dietary evaluation in agroecosystems. This work will enable future research to rapidly expand our knowledge on the diet preference and range of crops that pests consume in various agroecosystems, which will help in the redesign and development of new crop rotation regimes to minimize polyphagous pest pressure and damage on crops.


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