scholarly journals ShinyDiversity - Understanding Alpha and Beta Diversity through Interactive Visualizations

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 479
Author(s):  
Eric T. Leung ◽  
Roshan Noronha ◽  
Ali Mirza ◽  
Reva Shenwai ◽  
Asterios Mpatziakas
Keyword(s):  
Microbial Communities ◽  
Beta Diversity ◽  
Diversity Indices ◽  
Alpha And Beta Diversity ◽  
The Past ◽  
Interactive Visualizations ◽  
Interactive Application

In the past few decades, ecologists have developed many diversity indices to describe within and between sample diversity. Consequently, it can be difficult to determine which index to choose and how the distribution of microbial communities affect these indices. We've developed an interactive application, ShinyDiversity, that dynamically visualizes different alpha or beta diversity indices. In enabling users to select and simultaneously visualize different indices, our application aims to facilitate understanding of how the microbial data affects selected indices.

scholarly journals Diversity Indices of Plant Communities and Their Rhizosphere Microbiomes: An Attempt to Find the Connection

2021 ◽  
Vol 9 (11) ◽  
pp. 2339
Author(s):  
Aleksei O. Zverev ◽  
Arina A. Kichko ◽  
Aleksandr G. Pinaev ◽  
Nikolay A. Provorov ◽  
Evgeny E. Andronov
Keyword(s):  
Microbial Communities ◽  
Plant Communities ◽  
Plant Diversity ◽  
Beta Diversity ◽  
Mutual Influence ◽  
Plant Root ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Alpha And Beta Diversity ◽  
Highly Correlated

The rhizosphere community represents an “ecological interface” between plant and soil, providing the plant with a number of advantages. Despite close connection and mutual influence in this system, the knowledge about the connection of plant and rhizosphere diversity is still controversial. One of the most valuable factors of this uncertainty is a rough estimation of plant diversity. NGS sequencing can make the estimations of the plant community more precise than classical geobotanical methods. We investigate fallow and crop sites, which are similar in terms of environmental conditions and soil legacy, yet at the same time are significantly different in terms of plant diversity. We explored amplicons of both the plant root mass (ITS1 DNA) and the microbial communities (16S rDNA); determined alpha- and beta-diversity indices and their correlation, and performed differential abundance analysis. In the analysis, there is no correlation between the alpha-diversity indices of plants and the rhizosphere microbial communities. The beta-diversity between rhizosphere microbial communities and plant communities is highly correlated (R = 0.866, p = 0.01). ITS1 sequencing is effective for the description of plant root communities. There is a connection between rhizosphere communities and the composition of plants, but on the alpha-diversity level we found no correlation. In the future, the connection of alpha-diversities should be explored using ITS1 sequencing, even in more similar plant communities—for example, in different synusia.

scholarly journals The Fecal Bacterial Microbiota in Horses with Equine Recurrent Uveitis

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 745
Author(s):  
Michelle Martin de Bustamante ◽  
Diego Gomez ◽  
Jennifer MacNicol ◽  
Ralph Hamor ◽  
Caryn Plummer
Keyword(s):  
Beta Diversity ◽  
High Throughput Sequencing ◽  
Illumina Miseq ◽  
Diversity Indices ◽  
Rrna Gene ◽  
Linear Discriminant ◽  
Alpha And Beta Diversity ◽  
Bacterial Microbiota ◽  
Healthy Control ◽  
Equine Recurrent Uveitis

The objective of this study was to describe and compare the fecal bacterial microbiota of horses with equine recurrent uveitis (ERU) and healthy horses using next-generation sequencing techniques. Fecal samples were collected from 15 client-owned horses previously diagnosed with ERU on complete ophthalmic examination. For each fecal sample obtained from a horse with ERU, a sample was collected from an environmentally matched healthy control with no evidence of ocular disease. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. The relative abundance of predominant taxa, and alpha and beta diversity indices were calculated and compared between groups. The phyla Firmicutes, Bacteroidetes, Verrucomicrobia, and Proteobacteria predominated in both ERU and control horses, accounting for greater than 60% of sequences. Based on linear discriminant analysis effect size (LEfSe), no taxa were found to be enriched in either group. No significant differences were observed in alpha and beta diversity indices between groups (p > 0.05 for all tests). Equine recurrent uveitis is not associated with alteration of the gastrointestinal bacterial microbiota when compared with healthy controls.

scholarly journals Unimodal Relationships of Understory Alpha and Beta Diversity along Chronosequence in Coppiced and Unmanaged Beech Forests

Diversity ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 101 ◽  
Author(s):  
Sándor Bartha ◽  
Roberto Canullo ◽  
Stefano Chelli ◽  
Giandiego Campetella
Keyword(s):  
Beta Diversity ◽  
Management Practices ◽  
Multiple Scales ◽  
Forest Succession ◽  
Spatial Scales ◽  
Alpha Diversity ◽  
Structural Diversity ◽  
Diversity Indices ◽  
Alpha And Beta Diversity ◽  
Coppice Management

Patterns of diversity across spatial scales in forest successions are being overlooked, despite their importance for developing sustainable management practices. Here, we tested the recently proposed U-shaped biodiversity model of forest succession. A chronosequence of 11 stands spanning from 5 to 400 years since the last disturbance was used. Understory species presence was recorded along 200 m long transects of 20 × 20 cm quadrates. Alpha diversity (species richness, Shannon and Simpson diversity indices) and three types of beta diversity indices were assessed at multiple scales. Beta diversity was expressed by a) spatial compositional variability (number and diversity of species combinations), b) pairwise spatial turnover (between plots Sorensen, Jaccard, and Bray–Curtis dissimilarity), and c) spatial variability coefficients (CV% of alpha diversity measures). Our results supported the U-shaped model for both alpha and beta diversity. The strongest differences appeared between active and abandoned coppices. The maximum beta diversity emerged at characteristic scales of 2 m in young coppices and 10 m in later successional stages. We conclude that traditional coppice management maintains high structural diversity and heterogeneity in the understory. The similarly high beta diversities in active coppices and old-growth forests suggest the presence of microhabitats for specialist species of high conservation value.

scholarly journals Alpha and Beta-diversity of Microbial Communities Associated to Plant Disease Suppressive Functions of On-farm Green Composts

Agriculture ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 113 ◽  
Author(s):  
Catello Pane ◽  
Roberto Sorrentino ◽  
Riccardo Scotti ◽  
Marcella Molisso ◽  
Antonio Di Matteo ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Ecological Niches ◽  
Rrna Gene ◽  
Alpha And Beta Diversity ◽  
Length Polymorphisms ◽  
Differential Pattern ◽  
Curtis Dissimilarity ◽  
Underlying Mechanisms

Green waste composts are obtained from agricultural production chains; their suppressive properties are increasingly being developed as a promising biological control option in the management of soil-borne phytopathogens. The wide variety of microbes harbored in the compost ecological niches may regulate suppressive functions through not yet fully known underlying mechanisms. This study investigates alpha- and beta-diversity of the compost microbial communities, as indicators of the biological features. Our green composts displayed a differential pattern of suppressiveness over the two assayed pathosystems. Fungal and bacterial densities, as well as catabolic and enzyme functionalities did not correlate with the compost control efficacy on cress disease. Differences in the suppressive potential of composts can be better predicted by the variations in the community levels of physiological profiles indicating that functional alpha-diversity is more predictive than that which is calculated on terminal restriction fragments length polymorphisms (T-RFLPs) targeting the 16S rRNA gene. However, beta-diversity described by nMDS analysis of the Bray–Curtis dissimilarity allowed for separating compost samples into distinct functionally meaningful clusters and indicated that suppressiveness could be regulated by selected groups of microorganisms as major deterministic mechanisms. This study contributes to individuating new suitable characterization procedures applicable to the suppressive green compost chain.

scholarly journals Contrasting resistance and resilience of the coupled oxic and anoxic components of an experimental microbial ecosystem

2021 ◽  
Author(s):  
Marcel Suleiman ◽  
Frank Pennekamp ◽  
Yves Choffat ◽  
Owen L. Petchey
Keyword(s):  
Microbial Communities ◽  
Oxygen Concentration ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Bottom Layer ◽  
Light Limitation ◽  
Delayed Response ◽  
Light Conditions ◽  
Alpha And Beta Diversity ◽  
The Impact

Understanding how microbial communities as key drivers of global biogeochemical cycles respond to environmental change remains a critical challenge in microbial ecology. In this study, we used phototrophic oxic-anoxic micro-ecosystems to understand how aerobic and anaerobic lake analog communities responded towards stressful light removal. Continuous oxygen measurements and four snapshots of full-length 16S rRNA sequencing were performed to detect responses of oxygen concentration, and of alpha and beta diversity. In the top layer, oxygen concentration decreased significantly under light limitation, but showed almost complete resilience after normal light conditions were restored, while the bottom layer remained anoxic throughout the experiment. Microbial communities, however, differed in their response behavior: alpha-diversity of the aerobic communities showed a delayed response after light conditions were restored, and their composition was not resilient during the duration of the experiment. In contrast, alpha-diversity of the anaerobic bottom water communities increased due to the stressor and was resilient. Beta-diversity changed significantly during light removal, showed resilience for the aerobic communities, but stayed significantly affected for the anaerobic communities. We conclude that whole-ecosystem responses and several time-points are needed to fully understand the impact of stressors on microbial ecosystems, since resistance/resilience can differ among and within abiotic and biotic ecosystem components.

scholarly journals Ranking the Biases: The Choice of OTUs vs. ASVs in 16S rRNA Amplicon Data Analysis Has Stronger Effects On Diversity Measures Than Rarefaction and Similarity Threshold

2021 ◽  
Author(s):  
Marlène Chiarello ◽  
Mark McCauley ◽  
Sébastien Villéger ◽  
Colin R Jackson
Keyword(s):  
16S Rrna ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Taxonomic Composition ◽  
Shannon Index ◽  
Minimal Impact ◽  
Alpha And Beta Diversity ◽  
Methodological Choices ◽  
Similarity Threshold

Abstract BackgroundAdvances in the analysis of amplicon sequence datasets have introduced a methodological shift in how research teams investigate microbial biodiversity, away from the classification and downstream analyses of traditional operational taxonomic units (OTUs), and towards the usage of amplicon sequence variants (ASVs). While ASVs have several inherent properties that make them desirable compared to OTUs, questions remain as to the influence that these pipelines have on the ecological patterns being assessed, especially when compared to other methodological choices made when processing data (e.g. rarefaction) and computing diversity indices. ResultsWe compared the respective influences of using ASVs vs. OTU-based pipelines, rarefaction of the community table, and OTU similarity threshold (97% vs. 99%) on the ecological signals detected in freshwater invertebrate and environmental (sediment, seston) 16S rRNA data sets, determining the effects on alpha diversity, beta diversity and taxonomic composition. While the choice of OTU vs. ASV pipeline significantly influenced unweighted alpha and beta diversities and changed the ecological signal detected, weighted indices such as the Shannon index, Bray-Curtis dissimilarity, and weighted Unifrac scores were not impacted by the pipeline followed. By comparison, OTU threshold and rarefaction had a minimal impact effect on all measurements, although rarefaction improved overall signals, especially in OTU-based datasets. The identification of major classes and genera identified revealed significant discrepancies across methodologies. ConclusionWe provide a list of recommendations for the analysis of 16S rRNA amplicon data. We notably recommend the use of ASVs when analyzing alpha-diversity patterns, especially in species-rich or environmental samples. Abundance weighted alpha- and beta-diversity indices should also be preferred compared to ones based on the presence-absence of biological units.

Collecting parasitic Aculeata (Hymenoptera) from rice ecosystems of Tamil Nadu, India

2020 ◽  
Vol 12 (8) ◽  
pp. 15828-15834
Author(s):  
J. Alfred Daniel ◽  
K. Ramaraju
Keyword(s):  
Beta Diversity ◽  
Tamil Nadu ◽  
Wiener Index ◽  
Diversity Indices ◽  
Alpha And Beta Diversity ◽  
High Rainfall ◽  
Rice Ecosystems ◽  
Western Zone ◽  
Cauvery Delta

Surveys were conducted to explore the parasitic aculeate fauna in rice ecosystems of Tamil Nadu in 2015–2016 in three different rice growing zones, viz., the western zone, the Cauvery delta zone and the high rainfall zone.  The study recorded a total of 32 aculeates that represent 12 species under seven families belonging to three super families, viz., Apoidea (Apidae), Chrysidoidea (Bethylidae, Chrysididae, & Dryinidae), and Vespoidea (Mutillidae, Scoliidae, & Thiphiidae).  Alpha and beta diversity were computed for the three zones and the diversity indices (Simpson’s index, Shannon-Wiener index, Pielou’s index) revealed the high rainfall zone as the most diverse zone, with the Cauvery delta zone being the least diverse.  On comparing the species similarities using the Jaccard’s index in between the three zones taken in pairs, it was found that 42 per cent similarity existed between the western and Cauvery delta zone and 11 per cent similarity between high rainfall and Cauvery delta zones and 16 per cent similarity between the high rainfall and western zones.

scholarly journals Study on the diversity of epiphytic bacteria on corn and alfalfa using Illumina MiSeq/NovaSeq high-throughput sequencing system

2021 ◽  
Vol 71 (1) ◽  
Author(s):  
Meixiao Wu ◽  
Yuehua Wang ◽  
Yijing Wang ◽  
Xuefei Wang ◽  
Ming Yu ◽  
...  
Keyword(s):  
High Throughput ◽  
Beta Diversity ◽  
High Throughput Sequencing ◽  
Raw Materials ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Diversity Indices ◽  
Epiphytic Bacteria ◽  
Alpha And Beta Diversity ◽  
Paired End Sequencing

Abstract Purpose To investigate the diversity of the epiphytic bacteria on corn (Zea mays) and alfalfa (Medicago sativa) collected in Hengshui City and Xingtai City, Hebei Province, China, and explore crops suitable for natural silage. Methods The Illumina MiSeq/NovaSeq high-throughput sequencing system was used to conduct paired-end sequencing of the community DNA fragments from the surface of corn and alfalfa collected in Hengshui and Xingtai. QIIME2 and R software were used to sort and calculate the number of sequences and taxonomic units for each sample. Thereafter, the alpha and beta diversity indices at of species level were calculated, and the abundance and distribution of taxa were analyzed and compared between samples. Result At phylum level, the dominant groups were Proteobacteria (70%), Firmicutes (13%), Actinobacteria (9%), and Bacteroidetes (7%). Meanwhile, the dominant genera were Pseudomonas (8%), Acinetobacter (4%), Chryseobacterium (3%), and Hymenobacter (1%). Enterobacteriaceae (24%) were the most predominant bacteria in both the corn and alfalfa samples. Alpha diversity analysis and beta diversity indices revealed that the diversity of epiphytic microbial communities was significantly affected by plant species but not by region. The diversity and richness of the epiphytic bacterial community of alfalfa were significantly higher than those of corn. Conclusion This study contributes to the expanding knowledge on the diversity of epiphytic bacteria in corn and alfalfa silage and provides a basis for the selection of raw materials.

Structural and Bioactive Studies of Halogenated Constituents from Sponges

2020 ◽  
Vol 27 (14) ◽  
pp. 2335-2360 ◽  
Author(s):  
Chao Li ◽  
Dayong Shi
Keyword(s):  
Microbial Communities ◽  
Organic Compounds ◽  
Biological Activities ◽  
Marine Sponges ◽  
Nitrogen Compounds ◽  
Halogenated Organic Compounds ◽  
Bioactive Natural Products ◽  
The Past ◽  
Tyrosine Derivatives ◽  
Polyunsaturated Lipids

: Marine organisms are abundant sources of bioactive natural products. Among metabolites produced by sponges and their associated microbial communities, halogenated natural compounds accounted for an important part due to their potent biological activities. The present review updates and compiles a total of 258 halogenated organic compounds isolated in the past three decades, especially brominated derivatives derived from 31 genera of marine sponges. These compounds can be classified as the following classes: brominated polyunsaturated lipids, nitrogen compounds, brominated tyrosine derivatives and other halogenated compounds. These substances were listed together with their source organisms, structures and bioactivities. For this purpose, 84 references were consulted.

Sign in / Sign up

Export Citation Format

Share Document