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Nouvelles Recherches Sur la Distribution Florale
... For alpha-diversity analysis, the following two diversity indices, namely Shannon index (Shannon, 1948a,b;Shannon et al., 2003) and Simpson index (Simpson, 1949), were calculated for each sample by using QIIME2 software, and box plots were drawn to compare the abundance and homogeneity of ASVs among the samples. Betadiversity analyses were performed to determine changes in microbial community structure between samples (Lozupone and Knight, 2005;Lozupone et al., 2007), and the results were analyzed by principal coordinate analysis (PCoA) with the Bray-Curtis method (Bray and Curtis, 1957) and hierarchical clustering (UPGMA) (based on the Bray-Curtis method, unweighted UniFrac distance) (Jaccard, 1908;Lozupone and Knight, 2005) and weighted UniFrac distance method (Lozupone et al., 2007) for visualization. For determining species relationships, Cisco map analysis was performed using Genescloud tools, a free online platform for data analysis. ...
Introduction
Symbiotic microbial have a significant impact on the growth and metabolism of medicinal plants. Schisandra chinensis is a very functionally rich medicinal herb; however, its microbial composition and diversity have been poorly studied.
Methods
In the present study, the core microbiomes associated with the rhizospheric soil, roots, stems, leaves, and fruits of S. chinensis from six geographic locations were analyzed by a macro-genomics approach.
Results
Alpha and beta diversity analyses showed that the diversity of microbial composition of S. chinensis fruits did not differ significantly among the geographic locations as compared to that in different plant compartments. Principal coordinate analysis showed that the microbial communities of S. chinensis fruits from the different ecological locations were both similar and independent. In all S. chinensis samples, Proteobacteria was the most dominant bacterial phylum, and Ascomycota and Basidiomycota were the most dominant fungal phyla. Nitrospira, Bradyrhizobium, Sphingomonas, and Pseudomonas were the marker bacterial populations in rhizospheric soils, roots, stems and leaves, and fruits, respectively, and Penicillium, Golubevia, and Cladosporium were the marker fungal populations in the rhizospheric soil and roots, stems and leaves, and fruits, respectively. Functional analyses showed a high abundance of the microbiota mainly in biosynthesis.
Discussion
The present study determined the fungal structure of the symbiotic microbiome of S. chinensis, which is crucial for improving the yield and quality of S. chinensis.
... The numerical taxonomy and multivariate analysis system for personal computers, NTSYS-pc version 2.20 (Exeter Software), developed by Rohlf (1998), was used to read the data matrix. SIMQUAL (Similarity for Quantitative Data), a program, was used to analyze the data matrix using Jaccard's similarity coefficient ( Jaccard, 1908). The polymorphic information content (PIC) was calculated, according to the method of Miks and Binkowski (2018). ...
The experiment was conducted during July, 2020–January, 2021 at Agroforestry Research Station, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat, India. Annona belongs to the family Annonaceae. The Annonaceae fruits are morphologically uniform but each type has a unique taste, flavour pulp colour and texture. The study revealed three types of leaf shapes (ovate, elliptic and lanceolate), leaf apex (acute, rounded and obtuse), leaf base (acute, rounded and acuminate), fruit shape (cordate, rounded and irregular), medium and late time of harvest maturity, overlapping and smooth segmentation of the surface and only one type for fruit at peduncle end i.e., inflated. The biochemical analysis of Annona species revealed the ranges of TSS (18.39 to 28.32 °B), TA of pulp (0.18–0.80%), reducing sugar (15.02–19.44%), non-reducing sugar (2.77–5.92%), total sugar (17.79–23.70%), ascorbic acid (27.55–43.10 mg 100 g-1) and phenol (0.18–0.36%). The DNA was amplified using fourteen simple sequence repeats primers and twenty-six alleles were found with an average of 1.86 alleles loci-1. The polymorphism information content value of the SSR markers was in the range of 0.09 to 0.38. A dendrogram was developed based on the cluster analysis, which revealed similarity index values varied from 0.58 to 1.00 with an average of 0.83. Based on the dendrogram the genotypes were clustered into two main clusters viz., A and B. Cluster A has sixteen genotypes and cluster B has two genotypes belonging to different Annona species. These results concluded that SSR markers could be efficiently used to study divergence among Annona genotypes.
... Rarefaction curve analysis via the QIIME2 diversity plugin was used to estimate the completeness of microbial community sampling, using different sampling depth thresholds (5000, 10,000 and 20,000 reads per sample). Subsequently, alpha indices (Shannon's diversity index [25], number of observed OTUs, Faith's phylogenetic diversity [26] and Pielou's evenness [27]) and beta dissimilarities (Jaccard distance [28], Bray-Curtis distance [29] and unweighted and weighted UniFrac distances [30]) were calculated at the sample level. Principal coordinates analysis ("PCoA") plots were developed using the EMPeror application [31] for beta diversity metrics to check intra-and inter-group heterogeneity. ...
Growing evidence suggests that alterations in the gut microbiome impact the development of inflammatory bowel diseases (IBDs), including Crohn’s disease (CD) and ulcerative colitis (UC). Although IBD often requires the use of immunosuppressant drugs and biologic therapies to facilitate clinical remission and mucosal healing, some patients do not benefit from these drugs, and the reasons for this remain poorly understood. Despite advancements, there is still a need to develop biomarkers to help predict prognosis and guide treatment decisions. The aim of this study was to investigate the gut microbiome of IBD patients using biologics to identify microbial signatures associated with responses, following standard accepted criteria. Microbiomes in 66 stool samples from 39 IBD patients, comprising 20 CD and 19 UC patients starting biologic therapies, and 29 samples from healthy controls (HCs) were prospectively analyzed via NGS and an ensemble of metagenomics analysis tools. At baseline, differences were observed in alpha and beta metrics among patients with CD, UC and HC, as well as between the CD and UC groups. The degree of dysbiosis was more pronounced in CD patients, and those with dysbiosis exhibited a limited response to biological drugs. Pairwise differential abundance analyses revealed an increasing trend in the abundance of an unannotated genus from the Clostridiales order, Gemmiger genus and an unannotated genus from the Rikenellaceae family, which were consistently identified in greater abundance in HC. The Clostridium genus was more abundant in CD patients. At baseline, a greater abundance of the Odoribacter and Ruminococcus genera was found in IBD patients who responded to biologics at 14 weeks, whereas a genus identified as SMB53 was more enriched at 52 weeks. The Collinsella genus showed a higher prevalence among non-responder IBD patients. Additionally, a greater abundance of an unclassified genus from the Barnesiellaceae family and one from Lachnospiraceae was observed in IBD patients responding to Vedolizumab at 14 weeks. Our analyses showed global microbial diversity, mainly in CD. This indicated the absence or depletion of key taxa responsible for producing short-chain fatty acids (SCFAs). We also identified an abundance of pathobiont microbes in IBD patients at baseline, particularly in non-responders to biologic therapies. Furthermore, specific bacteria-producing SCFAs were abundant in patients responding to biologics and in those responding to Vedolizumab.
... TBI measures the change in species assemblages between the same site at different time points (Legendre, 2019). TBI values were calculated as dissimilarity (D) values using the Jaccard index and ranged from 0 -1, with values approaching 1 indicating that the two communities are completely dissimilar (Jaccard, 1908;Legendre, 2019;Magurran et al., 2019). While a-diversity can indicate broad changes in biodiversity such as the pool of species diversity, b-diversity measures calculated as TBI values also provide insight into the losses and gains of species that can indicate changes to community composition even when the number of species present remains the same . ...
Introduction
The diversity of freshwater fishes is threatened by multiple environmental stressors, including climate change, alterations in land use, and introduction of non-native species. However, the quantification of temporal biodiversity in freshwater communities is limited. Here, we asked: i) how has alpha (species richness), beta (changes in freshwater species composition), and gamma diversity (total species diversity in a landscape) changed over time for lakes over a 50 year period?; and ii) What are the climatic, land use, and lake morphological drivers associated with higher diversity?
Methods
We assembled a database of fish species occurrence from 20 lakes across subalpine and alpine regions in Alberta from 1970-2019, in addition to lake morphological, climatic, and land use characteristics of the watersheds.
Results
We observed an overall increase in alpha, beta, and gamma diversity from the 1970s to 2009s. However, all measures of diversity declined from 2010-2019. We found that more lakes and species assemblages were influenced by species gains, rather than species losses (with the exception of the last decade of sampling).
Discussion
Generally, we found that coolwater species were expanding and coldwater fishes were being lost throughout our study lakes. We highlight temporal heterogeneity in fish biodiversity responses to substantial environmental pressures in this region.
... Cuadro 1. Documentos oficiales analizados referentes a las directrices educativas nacionales de cada país. Finalmente, a partir de la cuantificación de temas para cada país se verificó la similitud entre estos, utilizando el índice de similitud de Jaccard (Jaccard, 1908). Este índice puede tomar un intervalo de 0% a 100%, donde valores altos de porcentaje indican una mayor similaridad entre los miembros del grupo analizado. ...
América Latina presenta amplia biodiversidad, multiculturalidad y problemáticas ambientales complejas. Sin embargo, la esfera educativa debe comprender la crisis ambiental desde una óptica interdisciplinar, proponiendo mecanismos que resuelvan este escenario emergencial. Esta investigación analizó la incorporación de dimensiones de la conservación en las directrices curriculares nacionales (DCN) de Ciencias y Biología en 20 países de América Latina. Fueron ponderados dos índices para comparar la calidad y el abordaje de la conservación en las DCN. Se encontraron 50 temas asociados a la conservación y los DCN fueron clasificados en diferentes categorías de conservación, con predominio de abordaje conservacionista o pragmática. Concluimos que es necesario fortalecer la calidad de la discusión curricular sobre la conservación en las escuelas de América latina.
... Cluster analysis was performed on the similarity coefficient matrix. The Jaccard similarity matrix was used for cluster analysis using Unweighted Pair Group Method of Arithmetic average (UPGMA) [27] into Numerical Taxonomy System of Multivariate Programs (NTSyspc) (version 2.10e) software package [28]. Exact size of DNA fragment was recorded for each variety and primer. ...
Mango (Mangifera indica L.) is an allotetraploid (2n = 4X= 40) drupe fruit and has high nutritional value belongs to genus Mangifera and family Anacardiaceae. Mango cultivars are used with worldwide acceptance to pharmacological, ethnomedical, and phytochemical industries. Assessment of the genetic distinctiveness of a cultivar through morphological descriptors is an important tool for both the registration and the protection. New mango genotypes have been improved using valuable diverse germplasm resources to ensure food security. DNA fingerprinting based simple sequence repeats (SSR)-markers have been the most broadly used, effective and accurate in evaluation of genetic characterization of a cultivar. Molecular breeding is an effective source of genetic gain after improvement of fruit trees using marker assisted genomic selection. Total genomic DNA (gDNA) was generated using CTAB method from each cultivar. The most effective 50 hyper-variable SSR markers were selected. Highly specific DNA fingerprints were identified in the candidate line ‘Azeem Chaunsa’ compared with three standard cultivars using SSR-PCR. An agglomerative hierarchical clustering method was used to construct dendrogram based on the UPGMA clustering method. Cultivar identification diagram (CID) was constructed to evaluate association among standard cultivars and Azeem Chaunsa. Our results showed that SSR markers could efficiently assess genetic diversity in mango. The genetic similarity coefficients were recorded between the cultivars of mango ranged from 0.49 to 0.67. CID results concluded that cultivar ‘Azeem Chaunsa’ varied significantly from the check cultivar, Sindhri (46.2%), S.B Chaunsa (45%) and Sufaid Chaunsa (46.7%). The results obtained in this study will orient cultivar identification strategies for a successful future.
... Cluster analysis was performed on the similarity coefficient matrix. The Jaccard similarity matrix was used for cluster analysis using Unweighted Pair Group Method of Arithmetic average (UPGMA) [27] into Numerical Taxonomy System of Multivariate Programs (NTSyspc) (version 2.10e) software package [28]. Exact size of DNA fragment was recorded for each variety and primer. ...
Mango (Mangifera indica L.) is an allotetraploid (2n = 4X= 40) drupe fruit and has high nutritional value belongs to genus Mangifera and family Anacardiaceae. Mango cultivars are used with worldwide acceptance to pharmacological, ethnomedical, and phytochemical industries. Assessment of the genetic distinctiveness of a cultivar through morphological descriptors is an important tool for both the registration and the protection. New mango genotypes have been improved using valuable diverse germplasm resources to ensure food security. DNA fingerprinting based simple sequence repeats (SSR)-markers have been the most broadly used, effective and accurate in evaluation of genetic characterization of a cultivar. Molecular breeding is an effective source of genetic gain after improvement of fruit trees using marker assisted genomic selection. Total genomic DNA (gDNA) was generated using CTAB method from each cultivar. The most effective 50 hyper-variable SSR markers were selected. Highly specific DNA fingerprints were identified in the candidate line ‘Azeem Chaunsa’ compared with three standard cultivars using SSR-PCR. An agglomerative hierarchical clustering method was used to construct dendrogram based on the UPGMA clustering method. Cultivar identification diagram (CID) was constructed to evaluate association among standard cultivars and Azeem Chaunsa. Our results showed that SSR markers could efficiently assess genetic diversity in mango. The genetic similarity coefficients were recorded between the cultivars of mango ranged from 0.49 to 0.67. CID results concluded that cultivar ‘Azeem Chaunsa’ varied significantly from the check cultivar, Sindhri (46.2%), S.B Chaunsa (45%) and Sufaid Chaunsa (46.7%). The results obtained in this study will orient cultivar identification strategies for a successful future.
Massive sequencing of a fragment of 16S rRNA gene allows the characterization of bacterial communities in different body sites: the microbiota. Nasal microbiota can be analyzed by DNA extraction from nasal swabs, amplification of the specific fragment of interest, and posterior sequencing. The raw sequences obtained need to go through a computational process to check their quality and then assign the taxonomy. Here, we will describe the complete process from sampling to get the microbial diversity of nasal microbiota in health and disease.
The inter simple sequence repeat (ISSR) marker was used in this study for genetic fingerprinting and identification of released chickpea varieties and for the determination of the genetic relationships among these cultivars. A total of 19 released chickpea varieties were subjected to ISSR analysis with the objective of evaluating the genetic diversity among the cultivars. A total of 20 ISSR primers were initially screened and later based on their reproducibility and polymorphism, four of them were selected for the molecular diversity assay. Amplification of genomic DNA of the 19 varieties using four ISSR primers produced 38 scorable fragments. On average, 9.5 polymorphic bands per primer were observed in ISSR analysis. The total number of bands amplified by 3' anchored primers varied from 7 to 12. The primers based on poly (GGAGA) and (AG)YT repeat motifs produced highest number of fragments (10 and 12, respectively), whereas, primers GACA and (GA)T, produced minimum number of fragments (7 and 9, respectively). Overall, 81.58% of the loci were polymorphic and 96.17 and 3.83% of variation were partitioned into within and among population, respectively. The least genetic similarity was recorded between the varieties, Shasho and Minjar (0.41), and highest genetic similarity (0.97) between the varieties, Worku and Kutaye. The UPGMA dendrogram clustered all genotypes into four different clusters and three varieties such as Shasho, Chefe and DZ-10-11 observed to be an out lie. The results indicate the presence of genetic diversity within released cultivars of chickpea in Ethiopia.
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