Universal Primers Research Articles

Taxonomic accuracy and complementarity between bulk and eDNA metabarcoding provides an alternative to morphology for biological assessment of freshwater macroinvertebrates

Determining biological status of freshwater ecosystems is critical for ensuring ecosystem health and maintaining associated services to such ecosystems. Freshwater macroinvertebrates respond predictably to environmental disturbances and are widely used in biomonitoring programs. However, many freshwater species are difficult to capture and sort from debris or substrate and morphological identification is challenging, especially larval stages, damaged specimens, or hyperdiverse groups such as Diptera. The advent of high throughput sequencing technologies has enhanced DNA barcoding tools to automatise species identification for whole communities, as metabarcoding is increasingly used to monitor biodiversity. However, recent comparisons have revealed little congruence between morphological and molecular-based identifications. Using broad range universal primers for DNA barcode marker cox1, we compare community composition captured between morphological and molecular-based approaches from different sources — tissue-based (bulk benthic and bulk drift samples) and environmental DNA (eDNA, filtered water) metabarcoding — for samples collected along a gradient of anthropogenic disturbances. For comparability, metabarcoding taxonomic assignments were filtered by taxa included in the standardised national biological metric IBMWP. At the family level, bulk benthic metabarcoding showed the highest congruence with morphology, and the most abundant taxa were captured by all techniques. Richness captured by morphology and bulk benthic metabarcoding decreased along the gradient, whereas richness recorded by eDNA remained constant and increased downstream when sequencing bulk drift. Estimates of biological metrics were higher using molecular than morphological identification. At species level, diversity captured by bulk benthic samples were higher than the other techniques. Importantly, bulk benthic and eDNA metabarcoding captured different and complementary portions of the community — benthic versus water column, respectively — and their combined use is recommended. While bulk benthic metabarcoding can likely replace morphology using similar benthic biological indices, water eDNA will require new metrics because this technique sequences a different portion of the community.

Development of Highly Efficient Universal Pneumocystis Primers and Their Application in Investigating the Prevalence and Genetic Diversity of Pneumocystis in Wild Hares and Rabbits.

Despite its ubiquitous infectivity to mammals with strong host specificity, our current knowledge about Pneumocystis has originated from studies of merely 4% of extant mammalian species. Further studies of Pneumocystis epidemiology across a broader range of animal species require the use of assays with high sensitivity and specificity. To this end, we have developed multiple universal Pneumocystis primers targeting different genetic loci with high amplification efficiency. Application of these primers to PCR investigation of Pneumocystis in free-living hares (Lepus townsendii, n = 130) and rabbits (Oryctolagus cuniculus, n = 8) in Canada revealed a prevalence of 81% (105/130) and 25% (2/8), respectively. Genotyping analysis identified five and two variants of Pneumocystis from hares and rabbits, respectively, with significant sequence divergence between the variants from hares. Based on phylogenetic analysis using nearly full-length sequences of the mitochondrial genome, nuclear rRNA operon and dihydropteroate synthase gene for the two most common variants, Pneumocystis in hares and rabbits are more closely related to each other than either are to Pneumocystis in other mammals. Furthermore, Pneumocystis in both hares and rabbits are more closely related to Pneumocystis in primates and dogs than to Pneumocystis in rodents. The high prevalence of Pneumocystis in hares (P. sp. 'townsendii') suggests its widespread transmissibility in the natural environment, similar to P. oryctolagi in rabbits. The presence of multiple distinct Pneumocystis populations in hares contrasts with the lack of apparent intra-species heterogeneity in P. oryctolagi, implying a unique evolution history of P. sp. 'townsendii' in hares.

Double-Tube Multiplex TaqMan Real-Time PCR for the Detection of Eight Animal-Derived Dairy Ingredients.

Milk and dairy products represent important sources of nutrition in our daily lives. The identification of species within dairy products holds importance for monitoring food adulteration and ensuring traceability. This study presented a method that integrated double-tube and duplex real-time polymerase chain reaction (PCR) with multiplex TaqMan probes to enable the high-throughput detection of animal-derived ingredients in milk and dairy products. The detection system utilized one pair of universal primers, two pairs of specific primers, and eight animal-derived specific probes for cow, buffalo, goat, sheep, camel, yak, horse, and donkey. These components were optimized within a double-tube and four-probe PCR multiplex system. The developed double-tube detection system could simultaneously identify the above eight targets with a detection limit of 10-0.1 pg/μL. Validation using simulated adulterated milk samples demonstrated a detection limit of 0.1%. The primary advantage of this method lies in the simplification of the multiplex quantitative real-time PCR (qPCR) system through the use of universal primers. This method provides an efficient approach for detecting ingredients in dairy products, providing powerful technical support for market supervision.

Influence of Varied Silane Commercial Brands and Adhesive Application on Bond Strength and Stability to Lithium Disilicate Glass Ceramic.

This study aimed to evaluate the impact of various commercial silane brands with varied chemical compositions with or without the application of an adhesive layer on the microshear bond strength and durability of a resin luting agent to lithium disilicate glass ceramic. Lithium disilicate glass ceramic discs (EMX, IPS e.max Press, Ivoclar Vivadent) measuring 10 mm in diameter and 3 mm in thickness were fabricated (n=240). Surfaces were etched using 5% hydrofluoric acid and randomly assigned to 10 groups based on the commercial brand of silane used (n=24): [RP] RelyX Ceramic Primer (3M ESPE); [PS] Prosil (FGM); [SA] Silano (Angelus); [SM] Silano (Maquira); [SU] Silane (Ultradent); [GL] GLUMA Ceramic Primer (Kulzer); [CB] Ceramic Bond (VOCO); [MB] Monobond N (Ivoclar Vivadent); [CP] Clearfil Ceramic Primer (Kuraray); and [DE] 2-step silane (Dentsply Sirona). Half of the EMXs (n=12) received a thin adhesive layer (+) after the silane and prior to resin luting agent, while the other half (n=12) did not receive an adhesive layer (-). For the microshear bond strength test (μSBS), four light-cured resin luting agent cylinders (1 mm in diameter) were created on each EMX surface. Half of these specimens were tested after 24 hours, while the other half were stored in deionized water for 6 months. The μSBS test was conducted using a universal testing machine (DL 500, EMIC) at a crosshead speed of 1 mm/min until failure. The obtained data underwent statistical analysis using analysis of variance (ANOVA) and the Tukey test (α=0.05). There was significant influence of the silane commercial brand on bond strength. Notably, "universal primers" yielded lower bond strength results compared to "pure" silane solutions. Water storage had a detrimental effect on microshear bond strength for certain silane commercial brands. Additionally, the application of an adhesive layer negatively impacted bond strength results for all silanes. This study confirms the importance of both silane commercial brand and chemical composition in relation to bond strength of resin luting agents to lithium disilicate glass ceramic. Furthermore, the application of an adhesive layer may have an adverse effect on bond stability over time.

Abstract 1121: Neutrophil Proteobacteria Sequences Increases After Open Aortic Surgery

Introduction: Bacterial extracellular vesicles (bEV) transport diverse cargoes, including nucleic acids, and play a crucial role during host-microbe interactions, including modifying host immune response. Neutrophil activation is prevalent in aortic disease pathogenesis, but the cause is unclear. The baseline neutrophilic bEV content and its dynamics are unknown and may provide insight into neutrophil activation in aortic disease. Research Question: Does open aortic surgery change neutrophil bEV content? Methods: Blood was collected pre and post-operatively from 6 patients undergoing open aortic surgery. Neutrophils were isolated using standard centrifugation techniques, and nucleic acids were purified. The V1-V3 16s rRNA segments were amplified with universal primers and sequenced using an Illumina MiSeq platform. Reads were processed in QIIME2 and aligned to reference banks of known bacterial sequences. Sequence abundance was analyzed with Kruskal-Wallis and Wilcoxon-rank tests. Results: The average patient age was 60.2 years, with 4 male patients and 4 current smokers. The most common phylum and genus represented in the neutrophil bacterial reads were Proteobacteria (Figure 1A) and Delftia , respectively. The relative abundance of Proteobacteria sequences increased overtime (p=0.042) from a median of 45.43% (IQR:35.3-52.0) to 70.8% (IQR:66.1-81.5, p=0.026) post-operatively, to 83.5% (IQR:60.7-89.7, p=0.004) on POD1 (Figure 1B). POD3 Proteobacteria sequence abundance was stable from POD1 at 81.4% (IQR:64.2-89.6). Conclusions: Neutrophils of patients with aortic disease rapidly change their bacterial sequence content in response to open aortic surgery. Bacteria in the phylum Proteobacteria change most dramatically and equilibrate between POD 1 and 3. Further studies will elucidate the impact changing bacterial sequence abundance and bEV content has on neutrophil activity and its relationship to disease pathogenesis.

Assessing the impacts of aquaculture on local fish communities using environmental DNA metabarcoding analysis

AbstractFish aquaculture potentially affects the local ecosystem through feed (leftovers) and feces. However, evaluation of its impacts on biodiversity, especially those of mobile organisms such as fish, is not straightforward. Here, we report a case study in which environmental DNA (eDNA) metabarcoding with MiFish universal primers for the 12S rRNA region of fish is used to detect and assess the impact of aquaculture on local fish communities. In Shizugawa Bay, Minamisanriku Town, Miyagi Prefecture, Japan, Oncorhynchus kisutch (coho salmon) is aquacultured in sea cages from November to July, but is absent from August to October. We conducted eDNA surveys in June, August, October, and December 2021 of water at depths of 5 m and 1 m above the bottom obtained from two sites, one approximately 100 m and the other approximately 2500 m from the nearest aquaculture site. The total number of operational taxonomic units (OTUs) detected was 122, with a maximum of 50 and a minimum of 10. With distance‐based redundancy analysis (dbRDA) and PERMANOVA applied to the eDNA‐based community compositional data, we detected a significant effect of the presence of O. kisutch aquaculture on fish biodiversity. The generalized linear model (GLM) applied to each detected OTUs indicated that the aquaculture was associated positively with Leucopsarion petersii (ice goby), and Oncorhynchus spp. and negatively with Chaenogobius annularis (forktongue goby). Environmental DNA metabarcoding surveys, combined with multivariate statics, are a promising tool to identify the dimension of biodiversity that human activity affects and would serve as a basic survey for sustainable use of the sea.

Abstract 1120: Untargeted 16s Ribosomal Rna Survey Of Microbial Communities In The Patient With Aneurysmal And Occlusive Aortic Disease

Introduction: Inflammation is a hallmark of aneurysmal disease, but the etiology for the inflammation is unknown. Previously, bacteria and bacterial nucleic acid sequences have been identified within abdominal aortic aneurysm tissue. However, only one study has taken an un-targeted approach to assess the diversity of species and no study has surveyed bacterial species across the various environments in patients with aortic disease. Research Question: Does the distribution of bacterial sequences differ between environments and by disease status in patients with abdominal aortic disease? Methods: Whole blood, acute (luminal) thrombus, chronic (medial/abluminal) thrombus, and aortic wall specimens were obtained from 14 patients undergoing open aortic surgery. Five patients had aneurysm disease and nine patients had aortic occlusive disease. Sequencing using universal primers targeting the V3 - V5 16s rRNA bacterial gene was performed. Reads were processed and aligned to reference banks using QIIME2 to the genus level. Results: The average patient age was 60.9 years with no significant difference in baseline demographics. Phyllobacterium was the most common genus identified in acute and chronic thrombus for aneurysmal and occlusive disease while pseudomonas was the most common genus identified in aortic wall. Chao1 alpha diversity was higher in aneurysmal aortic wall samples compared to occlusive disease (10.6 vs 6.6, p=0.047). On principle component analysis, samples from similar tissue environments cluster together with 16% of the sequence variation explained by the grouping (p=0.003, Figure 1). Conclusions: The diversity of bacterial sequences groups by microenvironment within patients with aortic disease, suggesting a spectrum of bacterial communities that progress from blood through the luminal thrombus to the aortic wall. Further work could distinguish genus level variations that associates with disease in the different environments.

First Report of 'Candidatus Phytoplasma asteris'-related Strain (16SrI group) Associated with Small Leaves, Leaf Yellowing, and Shoot Proliferation of Morning Glory (Ipomoea biflora) in Taiwan.

Ipomoea biflora L., commonly known as morning glory, is an herbaceous vine plant in the Convolvulaceae family and is widespread at low elevations in Taiwan and other East Asian countries. In September 2023, six I. biflora plants exhibiting small leaves, leaf yellowing, and shoot proliferation were observed in a vacant lot in Taiwan Agricultural Research Institute (TARI), Wufeng District, Taichung, Taiwan, representing 100% disease incidence in the area. All the symptomatic morning glory climbed onto Murraya paniculata L. (common jasmine orange) which however showed no similar symptoms. The total DNA (two samples for each plant) from leaf tissues of three symptomatic morning glory plants, two asymptomatic morning glory plants, and one asymptomatic common jasmine orange was isolated by the CTAB method (Fulton et al. 1995) and used for PCR with the universal primers, P1 (Deng and Hiruki 1991)/P7 (Schneider et al. 1995), to amplify a fragment containing partial 16S rDNA. Expected 1.8-kb bands were amplified from DNA extracted from all symptomatic plants, whereas no PCR product was detected from that of the asymptomatic I.biflora and M. paniculata plants. Six PCR products were cloned and sequenced in the Biotechnology Center DNA-sequencing facility at National Chung Hsing University, and one representative sequence was selected and deposited in GenBank. BLAST analysis revealed that the obtained 16S rDNA sequence (PP230905) shared 99.92% identity with the following phytoplasma strains: rapeseed phyllody phytoplasma (CP055264), plumbago auriculata leaf yellowing phytoplasma (MN239503), and aster yellows phytoplasma (MK992774), which all belong to the 16SrI subgroup. The query 16S rDNA sequence shares 99.84% identity with that of the 'Candidatus Phytoplasma asteris' reference strain (M30790), suggesting that the phytoplasma is a 'Ca. Phytoplasma asteris'-related strain. A virtual restriction fragment length polymorphism (RFLP) analysis was conducted using iPhyClassifier tool (Zhao et al. 2009), and the pattern derived from the 16S rDNA fragment of the I. biflora phytoplasma was identical (similarity coefficient 1.00) to the reference pattern of 16SrI, subgroup B (onion yellows phytoplasma OY-M; AP006628). Six total DNA samples from symptomatic plants were used as templates to amplify 842 bp secA sequences with SecAfor1 and SecArev3 primers (Hodgetts et al. 2008), and one representative sequence was deposited in GenBank. The partial secA sequence (PP263636) showed 98.22% identity with that of Trema levigatum witches'-broom phytoplasma (MW032212) that also belongs to the 16SrI group (Wan et al. 2021). Phylogenetic analysis of both 16S rDNA and secA confirmed I. biflora phytoplasma as 16SrI, subgroup B. Taken together, we concluded that the morning glory phytoplasma in this study was a 'Ca. Phytoplasma asteris'-related strain belonging to the 16SrI group. To the best of our knowledge, this is the first report of a phytoplasma-infected I. biflora in Taiwan, suggesting morning glory as a new natural host of 16SrI phytoplasmas, alongside other plants like roselle and citrus (Tseng et al. 2014; Feng et al. 2015).

Design and application of universal primers for mitochondrial genome sequencing of synanthropic mite species (Astigmatina: Acaridae)</p >

This study aims to design and develop a set of universal primers for amplification of the entire mitochondrial genome of Acaridae mites based on polymerase chain reaction (PCR). The conserved regions were screened by comparing the mitochondrial genomes of known Acaridae mites in GenBank. To ensure that the primers cover the entire mitochondrial sequence, the mitochondrial genome was divided into six overlapping fragments based on the conserved region. After synthesizing primers, we extracted the total DNA of Acaridae mites collected from grain stores. Then the total DNA of individual Acaridae mites was used as the template for PCR, Sanger sequencing, and sequence splicing. Agarose gel electrophoresis revealed that the lengths of the six amplification products were between 1.2 kb and 3.8 kb, consistent with design expectations. The resulting sequences could be successfully spliced to form a loop structure, confirming that the primers cover the entire mitochondrial genome. The splicing results were consistent with the full sequence released in GenBank. Developed universal primers can achieve rapid amplification and help to obtain mitochondrial genome from a single acarid mite with high efficiency.

First Report of Lingonberry Stunted Yellows Disease of Vaccinium vitis-idaea L. associated with 'Candidatus Phytoplasma trifolii'-Related Phytoplasma Strain in Lithuania.

Lingonberries (Vaccinium vitis-idaea L.) are low-growing, evergreen shrubs of cooler, northern regions of North America and Europe. These plants produce berries that are unique in flavor, bear high economic significance, and play a vital role in maintaining the diversity of the northern ecosystems (Kowalska, 2021). In October 2023 diseased plants of lingonberry were discovered in Labanoras Forest (55°14'N 25°42'E) (Lithuania). The plants expressed symptoms of stunting, yellowing, little leaf, shortened internodes, and stem distortions. Samples (leaves) were collected and tested from ten asymptomatic and ten symptomatic lingonberry plants. Total genomic DNAs of all samples were extracted by a CTAB protocol. Extracted DNAs were used as a template in direct and nested PCRs using the universal primer pairs P1/P7 and R16F2n/R2, respectively, to amplify phytoplasma 16S rRNA gene 1.2 kb fragments (Lee et al. 1998). The primer pairs SecAFor1/SecARev3 and SecAFor2/SecARev3 were used in direct and semi-nested PCRs, respectively, to amplify phytoplasma secA genes 0.5 kb fragment (Dickinson and Hodgetts, 2013). PCR amplicons of the 16S rRNA and secA genes specific for the phytoplasmas were only obtained from all sampled symptomatic plants. Three R16F2n/R2 and three SecAFor2/SecARev3 amplicons were cloned and submitted for Sanger sequencing (Nature Research Centre, Vilnius, Lithuania by 3500 Genetic Analyser). The three 16S rDNAs as well as the three secA gene fragments were identical. The BLAST analysis (NCBI) of the obtained sequences showed a similarity percentage, ranging from 99.75% to 100% (1247-1250 bp from 1250 bp) for 16SrRNA, and 98.13% to 99,15% (473-478 bp from 482 bp) for secA amplicons, with numerous strains of 'Candidatus (Ca.) Phytoplasma (P.) trifolii' (first hit MT674293 and KR906724, respectively). Additionally, 16S rDNA sequences by using iPhyClassifier were used to create virtual RFLP pattern (Zhao et al. 2009). The generated pattern was identical (similarity coefficient 1.00) to the reference pattern of 16Sr group VI, subgroup A. The phytoplasma strain detected in lingonberries was designated as lingonberry stunted yellows, LingbSY. Furthermore, the enzymatic RFLP analysis was performed with the 14 restriction enzymes (Lee et al., 1998), and obtained profiles were compared with virtually generated using iPhyClassifier. This yielded the same classification of detected phytoplasma to the 16SrVI-A phytoplasma subgroup. The phylogenetic analysis of both marker gene sequences revealed the same LingbSY phytoplasma classification. Selected sequences were deposited in GenBank (NCBI) with Accession No: PP237769 (16S rRNA gene) and No: PP238489 (secA gene). Phytoplasmas of 16SrI phytoplasma group were identified in lingonberries in Canada (Brochu et al. 2022). Strains of 16SrVI phytoplasma group were reported in Vaccinium myrtillus in Austria (Fernandez et al. 2007). This is the first report of 'Ca. P. trifolii' strain belonging to 16SrVI-A phytoplasma subgroup infecting lingonberry worldwide. Also, this is the first report of 16SrVI phytoplasma group in Lithuania. The presence of this phytoplasma poses a threat to the natural ecosystem and could eventually spread into agricultural settings in our country. Therefore, it's crucial to conduct surveillance for insect vectors, and assess effective control methods. Without proactive action, long term sustainability of lingonberries and their ecosystems may be jeopardized.

Whole genome sequence of Lactiplantibacillus plantarum strain HA9 isolated from conventional Iraqi cheese: First report

Background: Lactiplantibacillus plantarum is a renowned probiotic known for its ability to enhance health when ingested in sufficient quantities. While L. plantarum typically exhibits unique characteristics, variations in strains and environments can occur. Therefore, it is crucial to conduct genetic identification of the strain before incorporating it into products or administering it for health benefits.Methods: After being isolated from classic artisanal milk cheeses, the bacterial DNA extraction kit from GENEAID, Korea, was used, and strain HA9's genomic DNA was isolated. Then, the highly conserved section of ribosomal RNA was amplified with universal primers. The results were confirmed by a blast analysis of the NCBI database. The genome of HA9 was sequenced using the Illumina and PacBio Sequel II technologies (HN00194138; Psomagen/USA). The Prokaryotic Dynamic Programming Gene-Finding Algorithm software was applied to forecast coding genes. The Pathosystems Resource Integration Center constructed the L. plantarum genome.Result: According to the findings, the genome of the L. plantarum HA9 strain has a length of 3,321,986 bp and a GC percentage of 44.40. This assembled genome contained a total of 1,420 coding proteins and 82 contigs, as discovered by the Comprehensive Genome Analysis. The isolate had been submitted to the NCBI and received the HA9 genome sequence (accession ID: JAUTDL000000000.1).Conclusion Microbes' whole-genome sequencing plays a crucial role in clarifying their probiotic properties and enables accurate identification down to the strain level. The authors argue that further research should be done on probiotics' whole genomes, with a special emphasis on second-generation strains.Keywords: Lactiplantibacillus plantarum; Probiotics; Whole genome sequencing

Optimizing Akkermansia muciniphila Isolation and Cultivation: Insights into Gut Microbiota Composition and Potential Growth Promoters in a Chinese Cohort.

The study aims to analyze the composition of the gut microbiota in Chinese individuals using metagenomic sequencing technology, with a particular focus on the abundance of Akkermansia muciniphila (Akk). To improve the efficiency of Akk isolation and identification accuracy, modifications were made to the enrichment culture medium and 16S rRNA universal primers. Additionally, potential growth-promoting factors that stimulate Akk growth were explored through in vitro screening. The research results revealed that the abundance of Akk in Chinese fecal samples ranged from 0.004% to 0.4%. During optimization, a type of animal protein peptide significantly enhanced the enrichment efficiency of Akk, resulting in the isolation of three Akk strains from 14 fecal samples. Furthermore, 17 different growth-promoting factors were compared, and four factors, including galactose, sialic acid, lactose, and chitosan, were identified as significantly promoting Akk growth. Through orthogonal experiments, the optimal ratio of these four growth-promoting factors was determined to be 1:1:2:1. After adding 1.25% of this growth-promoting factor combination to the standard culture medium, Akk was cultivated at 37° for 36 h, achieving an OD600nm value of 1.169, thus realizing efficient proliferation and optimized cultivation of Akk. This study provides important clues for a deeper understanding of the gut microbiota composition in Chinese individuals, while also offering effective methods for the isolation and cultivation of Akk, laying the groundwork for its functional and application research in the human body.

Molecular detection and characterization of prevailing Theileria equi genotype in equine from northern India

Equine piroplasmosis caused by Theileria equi is a febrile, tick-borne disease of equids. However, there is limited literature about the genotyping of T. equi in India. Blood samples were collected from 202 horses and subjected to microscopy and PCR to detect T. equi. Initially, a universal screening primer pair targeting 18S ribosomal RNA genes common for Babesia caballi and T. equi was employed to amplify the DNA of both parasites. Thereafter additional primers were employed for species-specific detection resulting in amplification of approximately 435 bp specific for T. equi. T.equi was detected in 9.9% and 20.79% of horses screened by microscopy and PCR, respectively. The representative samples confirmed positive by PCR were sequenced, submitted to NCBI (OR651254, OR687254, OR685656, OR650830, OR650834), and used for genotype characterization and phylogenetic analysis. Employing Genetool and MEGA X software, the T. equi Indian isolates and across the globe were compared, and the results demonstrated 99.05–100% and 95.86–100% homologies, respectively. All the T. equi Indian isolates belonged to genotype A. Phylogeny based on the EMA-1 gene of five isolates (OR731831, OR731833, OR731829, OR731830, OR731832) were also characterized by sequencing and support the previous findings. Genotypes C and D, as well as genotypes B and E, exhibited lower levels of evolutionary divergence compared to other genotypes. The EMA-1 gene exhibited limited diversity and might not be the most suitable target for assessing variability within T. equi populations. The findings also reveal a significant association (p < 0.01) between T. equi infection and the presence of ticks.

Prevalence of strain (R and C strains) of fall armywormSpodoptera frugiperda in eastern India

An invasive alien pest, fall armyworm has been recently introduced to India. To date, two strains of FAW have been documented, viz. R strain (rice) and C strain (corn) without any clear biological attributes, even though differences are evident. A survey was conducted during 2020–22 over 18 field visits across the eastern part of India (Bihar, West Bengal, Orissa and Jharkhand) to isolate the genetic diversification of FAW populations collected from maize. This investigation was done with a mitochondrial-based ‘universal primer’ using mtCOI (mitochondrial cytochrome c oxidase subunit I) sequence analyses revealed that both strains (R strain and C strain) were present with the FAW. Interestingly, our comprehensive analysis indicates the dominance of the R strain over the C strain in the sample collected from the eastern part of India. This would be the first report from the eastern part of India, mainly the regions of Bihar, West Bengal, Orissa and Jharkhand, where FAW primarily feeds on maize. This study generates an idea about a probable incursion by a genetic asset of FAW in India, which needs dissection of the haplotype.

Genetic Diversity of Mangrove and Nypa Palm Species in the Niger Delta, Nigeria

Mangroves and nypa palm are two dominant coastal vegetation in the Niger delta that are sources of numerous ecosystem services. We thus hypothesized that both species are monophyletic, which means they are identical by descent. We began the study by randomly collecting fresh leave samples of nypa palm in a mixed forest comprising nypa palm and mangrove at a coastal community called Eagle Island. We put the leaves samples in zip lock bags containing silica gel crystals and transported them to the laboratory, where the DNA of the leaves was extracted. A quick-DNA plant/seed miniprep kit (Zymo-research Lab, California, USA). A total of six primer pairs were used for the amplification, namely: three microsatellite markers and three universal primers. Fragments of the samples were sequenced using the Ninagen, Brilliant DyeTM Terminator Cycle Sequencing kit V3.1 BRD3-100/1000. All three samples of the nypa palm were amplified, and the BLAST prediction tool was used to produce the new species. Our results show that out of the three samples sequenced (NI, N2, and N3), the N1 sample was identified as Nypa fruticans with 100% identity (Accession Number is KT312925.1), while the others were the new strains identified in the study namely N2 identified as Astrocaryum aculeatum with 98.95% identity (Accession Number is NC 044482.1) and N3 identified as Astrocaryum aculeatum with 99.21% (Accession Number is 044482.1).

Isolation, screening and characterization of efficient cellulose-degrading fungal and bacterial strains and preparation of their consortium under in vitro studies.

In this investigation, cellulose-degrading fungi and bacteria were isolated from different partially decomposed cellulose-rich substrates, such as groundnut residues, rice straw, and rotten wood, following dilution plating techniques on carboxymethyl cellulose agar media and screening for potential cellulose degradation ability. The development of a clear halo zone surrounding the microbial colonies during the initial screening process using the Congo red test (20 isolates) suggested cellulose hydrolysis, and the highest cellulase production activity was implied by the isolates with the largest clear zone ratio (9 isolates). Using both macroscopic and microscopic examinations, as well as standard biochemical tests outlined in Bergey's Manual of Determinative Bacteriology, the genus-level identification of fungi and bacteria was accomplished. In order to molecularly identify the 4 isolatedfungal and bacterial strains at the species level after being ultimately selected for cellulase production potential under in vitro studies, fungal and bacterial DNA was extracted and amplified by PCR using the universal primers ITS1 and ITS4 for fungi (ITS rRNA, 5.8S rRNA) and 8F and 1492R for bacterial isolates (16S rRNA). After sequencing, the PCR results were compared to other comparable sequences in GenBank (NCBI). Based on the available NCBI data, phylogenetic analysis of their ribosomal gene partial sequences revealed that DAJ2 (PP086700) shares 100% homology with Aspergillus foetidus, DTJ4 (PP086699) shares 99.74% similarity with Trichoderma atrobrunnium, DBJ6 (PP082584) shares 100% identity with Priestia megaterium, and DMB9 (PP082585) shares 99.88% homology with Micrococcus yunnanensis. The cellulolytic potential of Phanerochaete chrysosporium is well established. Therefore, it was considered a standard culture for comparison and was collected from the MTCC, Chandigarh, India. Overall, all 4 selected isolates and the check organism were mutually compatible or synergistic with each other, and their consortium is useful for the accelerated decomposition of organic constituents during rapid composting.

Multiplex fluorescent amplification-refractory mutation system PCR method for the detection of 10 genetic defects in Holstein cattle and its comparison with the KASP genotyping assay.

The common deleterious genetic defects in Holstein cattle include haplotypes 1-6 (HH1-HH6), haplotypes for cholesterol deficiency (HCD), bovine leukocyte adhesion deficiency (BLAD), complex vertebral malformation (CVM) and brachyspina syndrome (BS). Recessive inheritance patterns of these genetic defects permit the carriers to function normally, but homozygous recessive genotypes cause embryo loss or neonatal death. Therefore, rapid detection of the carriers is essential to manage these genetic defects. This study was conducted to develop a single-tube multiplex fluorescent amplification-refractory mutation system (mf-ARMS) PCR method for efficient genotyping of these 10 genetic defects and to compare its efficiency with the kompetitive allele specific PCR (KASP) genotyping assay. The mf-ARMS PCR method introduced 10 sets of tri-primers optimized with additional mismatches in the 3' end of wild and mutant-specific primers, size differentiation between wild and mutant-specific primers, fluorescent labeling of universal primers, adjustment of annealing temperatures and optimization of primer concentrations. The genotyping of 484 Holstein cows resulted in 16.12% carriers with at least one genetic defect, while no homozygous recessive genotype was detected. This study found carrier frequencies ranging from 0.0% (HH6) to 3.72% (HH3) for individual defects. The mf-ARMS PCR method demonstrated improved detection, time and cost efficiency compared with the KASP method for these defects. Therefore, the application of mf-ARMS PCR for genotyping Holstein cattle is anticipated to decrease the frequency of lethal alleles and limit the transmission of these genetic defects.

In silico assessment of 18S rDNA metabarcoding markers for the characterization of nematode communities.

Nematodes are keystone actors of soil, freshwater and marine ecosystems, but the complexity of morphological identification has limited broad-scale monitoring of nematode biodiversity. DNA metabarcoding is increasingly used to assess nematode diversity but requires universal primers with high taxonomic coverage and high taxonomic resolution. Several primers have been proposed for the metabarcoding of nematode diversity, many of which target the 18S rRNA gene. In silico analyses have a great potential to assess key parameters of primers, including taxonomic coverage, resolution and specificity. Based on a recently-available reference database, we tested in silico the performance of fourteen commonly used and one newly optimized primer for nematode metabarcoding. Most primers showed very good coverage, amplifying most of the sequences in the reference database, while four markers showed limited coverage. All primers showed good taxonomic resolution. Resolution was particularly good if the aim was the identification of higher-level taxa, such as genera or families. Overall, species-level resolution was higher for primers amplifying long fragments. None of the primers was highly specific for nematodes as, despite some variation, they all amplified a large number of other eukaryotes. Differences in performance across primers highlight the complexity of the choice of markers appropriate for the metabarcoding of nematodes, which depends on a trade-off between taxonomic resolution and the length of amplified fragments. Our in silico analyses provide new insights for the identification of the most appropriate primers, depending on the study goals and the origin of DNA samples. This represents an essential step to design and optimize metabarcoding studies assessing nematode diversity.

Identification of Indigenous Lactobacillus fermentum by 16S rRNA Gene Sequencing Isolated from Two Different Ecosystems: Newborn Infants and Bee’s Intestine

Background: The consumption of functional ferments that have functional characteristic sand contributes enormously to the safety and quality of food by offering several nutritional, technological and health properties. Lactobacillus fermentum (Lb. fermentum) is a Gram-positive bacterium belonging to the genus Lactobacillus and many are said to have the effect of preventing gastro-intestinal infections and improving immunological response. Additionally, Lb. fermentum produces diverse and potent antimicrobial peptides which can be applied as alternatives to antibiotics. Methods: In this study, samples were isolated from two different ecological niches, the first was feces of newborn infants (0-3 months) and the second from bee’s intestine, from south of Algeria : Ghardaïa 32°29'00" North, 3°41'00" East. Two indigenous lactic acid bacteria were isolated and evaluated for their probiotic properties. The isolate identification by sequencing 16S r DNA was performed using the universal primers 27F and 1492R. The NCBI Gen Bank database was used to have similarity of species. Result: The cultures showed good survival in simulated transit fluids as well as high acid and bile tolerance. The isolates also demonstrated antibacterial activity against Escherichia coli and Staphylococcus aureus, the inhibition zone was measured between 10 mm and 20 mm of diameter respectively. Comparing the sequences of the isolates with the Gen Bank database (NCBI), a high percentage with species of Lactobacillus fermentum was shown.

First report of Sclerotium hydrophilum causing leaf spot on Brasenia schreberi in central China.

Brasenia schreberi, commonly known as watershield and referred to as 'Chun Cai' in Chinese, is a worldwide aquatic vegetable. It has long been regarded as health- promoting vegetable due to production of mucilage in young shoots, and thus has gained popularity in China. In September 2022, a leaf spot disease was observed at the National Aquatic Vegetable Germplasm Resource Nursery located in Wuhan, Hubei province, China. The disease occurred on watershield leaves. It started with the formation of leaf spots surrounded by halos.These spots ranged in color from yellow to brown and in diameter from 1 to 10 mm. Subsequently, the smaller spots merged, ultimately causing the entire leaves to turn black. Small brown- to black-colored sclerotia were produced on the underside of the diseased leaves. Disease incidence was 30% on average, and yield loss was approximately 15% on average. To isolate the pathogen, leaf tissues at the disease-healthy border area were excised into 5 × 5 mm pieces, these segments were immersed in 75% ethanol for 30 s, followed by immersion in 0.5% sodium hypochlorite for 30 s, and then rinsed twice in sterile water. After air-drying, the leaf pieces were incubated on potato dextrose agar (PDA) in darkness at 28°C for 3 d. Mycelia from the leaf pieces were transferred to new PDA plates for purification, three sclerotia-forming fungal isolates (Whcc-1, Whcc-3, Whcc-4) were finally obtained. They were incubated on PDA at 28°C for 4 to 14 d for observation of colony morphology. At 4 d after incubation (DAI), they grew rapidly with the average growth rate of 2.2 cm/d and formed colonies with whitish substrate mycelia and well-developed aerial mycelia and small white to light brown-colored sclerotia. At 10 to 14 DAI, the sclerotia gradually turned to black, 0.2 to 0.4 mm in diameter (0.26 mm on average, n = 50). These morphological characteristics matched description of Sclerotium hydrophilum (Bashyal et al. 2021). Molecular identification was done to further clarify the species identity of this fungus. Genomic DNA was extracted from isolates Whcc-1, Whcc-3, and Whcc-4. The internal transcribed spacer region of the ribosomal DNA (ITS-5.8S rDNA) and the small subunit ribosomal RNA gene (ssrRNA) were amplified using universal primers ITS1/ITS4 and NS1/NS6, as described by White et al. (1990). Sequence analysis revealed a high degree of similarity between the ITS-5.8S rDNA sequences from Whcc-1, Whcc-3, and Whcc-4 (GenBank Acc. No. OP782030, PP035994, and PP035995, respectively) and those of S. hydrophilum strain CBS201.27 (GenBank Acc. No. FJ231396), with similarities of 99.25%, 99.4%, and 99.25%, respectively. The ssrRNA sequences from Whcc-1, Whcc-3, and Whcc-4 (GenBank Acc. No. PP238401, PP261342 and PP261345) were found to be identical, displaying 100% similarity to the ssrRNA sequences of S. hydrophilum strain ZH11 (GenBank Acc. No. KC354147). Based on both morphological and molecular evidence, it can be inferred that Whcc-1, Whcc-3, and Whcc-4 belong to the species S. hydrophilum. Pathogenicity tests were conducted by inoculation of the mycelial agar plugs of Whcc-1, Whcc-3 or agar plugs of fresh PDA (control) on floating leaves of two watershield plants, 4 leaves (replicates) for each treatment. After inoculation, the treated leaves were sealed in plastic bags to maintain humidity, and grown under natural conditions (18°C to 28°C, with 8 hours of light daily). At 7 DAI, while control leaves remained healthy, the leaves inoculated with Whcc-1 and Whcc-3 leaves formed yellow- to brown-colored spots similar to those observed in the field surveys. S. hydrophilum was re-isolated from the leaf spots, thus verifing Koch's postulates. S. hydrophilum has a wide host range, infecting at least 19 genera of plants, including common rice and wild rice (Johnson et al. 1976), and water lily (Kernkamp et al. 1977). Moreover, it has been reported to infect rice in China (Punter et al. 1984; Zhong et al. 2018). To our knowledge, this is the first report of S. hydrophilum on watershield leaves in central China.