scholarly journals The quest for absolute abundance: the use of internal standards for DNA-based microbial and community ecology

2020 ◽  
Author(s):  
Joshua Harrison ◽  
W. John Calder ◽  
Bryan N. Shuman ◽  
C. Alex Buerkle
Keyword(s):  
Community Ecology ◽  
Relative Abundance ◽  
Compositional Data ◽  
Direct Measure ◽  
Absolute Abundance ◽  
Internal Standards ◽  
Integral Component ◽  
Dna Pools ◽  
Relative Abundances ◽  
Sequencing Process

To characterize microbiomes and other ecological assemblages, ecologists routinely sequence and compare loci that differ among focal taxa. Counts of these sequences convey information regarding the occurrence and relative abundances of taxa, but provide no direct measure of their absolute abundances, due to the technical limitations of the sequencing process. The relative abundances in compositional data are inherently constrained and difficult to interpret. The incorporation of internal standards (ISDs; colloquially referred to as ``spike-ins'') into DNA pools can ameliorate the problems posed by relative abundance data and allow absolute abundances to be approximated. Unfortunately, many laboratory and sampling biases cause ISDs to underperform or fail. Here, we discuss how careful deployment of ISDs can avoid these complications and be an integral component of well-designed studies seeking to characterize ecological assemblages via sequencing of DNA.

scholarly journals propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis

2017 ◽  
Author(s):  
Thomas Quinn ◽  
Mark F. Richardson ◽  
David Lovell ◽  
Tamsyn Crowley
Keyword(s):  
Data Analysis ◽  
Relative Abundance ◽  
Compositional Data ◽  
Life Sciences ◽  
Genomic Data ◽  
R Package ◽  
Compositional Data Analysis ◽  
Computationally Efficient ◽  
Abundance Data ◽  
Relative Abundances

AbstractIn the life sciences, many assays measure only the relative abundances of components for each sample. These data, called compositional data, require special handling in order to avoid misleading conclusions. For example, in the case of correlation, treating relative data like absolute data can lead to the discovery of falsely positive associations. Recently, researchers have proposed proportionality as a valid alternative to correlation for calculating pairwise association in relative data. Although the question of how to best measure proportionality remains open, we present here a computationally efficient R package that implements two proposed measures of proportionality. In an effort to advance the understanding and application of proportionality analysis, we review the mathematics behind proportionality, demonstrate its application to genomic data, and discuss some ongoing challenges in the analysis of relative abundance data.

scholarly journals The quest for absolute abundance: The use of internal standards for DNA‐based community ecology

2020 ◽  
Vol 21 (1) ◽  
pp. 30-43 ◽  
Author(s):  
Joshua G. Harrison ◽  
W. John Calder ◽  
Bryan Shuman ◽  
C. Alex Buerkle
Keyword(s):  
Community Ecology ◽  
Absolute Abundance ◽  
Internal Standards

scholarly journals Parameter Identifiability of the Generalized Lotka-Volterra Model for Microbiome Studies

2018 ◽  
Author(s):  
Christopher H Remien ◽  
Mariah J Eckwright ◽  
Benjamin J Ridenhour
Keyword(s):  
Time Series ◽  
Relative Abundance ◽  
Population Dynamic ◽  
Dynamic Models ◽  
Volterra Model ◽  
Sufficient Information ◽  
Absolute Abundance ◽  
Abundance Data ◽  
Relative Abundances ◽  
Over Time

AbstractBackgroundPopulation dynamic models can be used in conjunction with time series of species abundances to infer interactions. Understanding microbial interactions is a prerequisite for numerous goals in microbiome research; predicting how populations change over time, determining how manipulations of microbiomes affect dynamics, and designing synthetic microbiomes to perform tasks are just a few examples. As such, there is great interest in adapting population dynamic theory for microbial systems. Despite the appeal, numerous hurdles exist. One hurdle is that the data commonly obtained from DNA sequencing yield estimates of relative abundances, while population dynamic models such as the generalized Lotka-Volterra model track absolute abundances or densities. It is not clear whether relative abundance data alone can be used to infer parameters of population dynamic models such as the Lotka-Volterra model.ResultsWe used structural identifiability analyses to determine the extent to which time series of relative abundances can be used to parameterize the generalized Lotka-Volterra model. We found that only with absolute abundance data to accompany relative abundance estimates from sequencing can all parameters be uniquely identified. However, relative abundance data alone do contain information on relative interaction strengths, which is sufficient for many studies where the goal is to estimate key interactions and their effects on dynamics. Our results also indicate that the relative interaction rates that can be estimated using relative abundance data provide ample information to estimate relative changes of absolute abundance over time. Using synthetic data for which we know the underlying structure, we found our results to be robust to modest amounts of both process and measurement error.ConclusionsFitting the generalized Lotka-Volterra model to time-series sequencing data typically requires either assuming a constant population size or performing additional measurements to obtain absolute abundances. We have found that these assumptions are not strictly necessary because relative abundance data alone contain sufficient information to estimate relative rates of interaction, and thus to infer key drivers of microbial population dynamics.

Abundance of Boeckella gracilis (Daday, 1902) (Copepoda, Calanoida) in seasonal coastal pools in the Araucania region (38°S, Chile)

Crustaceana ◽  
2018 ◽  
Vol 91 (10) ◽  
pp. 1211-1217
Author(s):  
Patricio De los Ríos
Keyword(s):  
Correlation Analysis ◽  
Environmental Stress ◽  
Relative Abundance ◽  
Calanoid Copepod ◽  
Inverse Correlation ◽  
Inland Waters ◽  
Absolute Abundance ◽  
Significant Inverse Correlation

Abstract The presence of the calanoid copepod Boeckella gracilis (Daday, 1902) in Chilean seasonal pools has been only poorly studied as yet. The aim of the present study thus is to investigate the role of conductivity and temperature on the relative and absolute abundance of B. gracilis in seasonal coastal pools in the Araucania region (38°S, Chile). The results of correlation analysis revealed the presence of a significant inverse correlation between conductivity and relative abundance, whereas no significant correlations were found between conductivity and absolute abundance, between temperature and absolute abundance, and between temperature and relative abundance. These results agree partially with similar observations for mountain pools in the same region, but they would not agree with observations for calanoids of saline and subsaline inland waters in the northern and southern extremes of Chile. Considering this scenario, the species would show different populational responses to environmental stress in different situations, which phenomenon deserves to be studied more extensively and in more detail.

scholarly journals Paleoenvironmental and paleobiological origins of coccolithophorid genusWatznaueriaemergence during the late Aalenian–early Bajocian

Paleobiology ◽  
2015 ◽  
Vol 41 (3) ◽  
pp. 415-435 ◽  
Author(s):  
Baptiste Suchéras-Marx ◽  
Emanuela Mattioli ◽  
Fabienne Giraud ◽  
Gilles Escarguel
Keyword(s):  
Marine Invertebrate ◽  
Time Interval ◽  
Calcareous Nannofossils ◽  
Calcareous Nannoplankton ◽  
Absolute Abundance ◽  
The Pacific ◽  
Relative Abundances ◽  
The Absolute ◽  
Oceanic Plates ◽  
Central Atlantic

AbstractThe latest Aalenian–early Bajocian time interval (ca. 171-169 Ma) is marked by a global reorganization of oceanic plates with the Central Atlantic opening and the formation of the Pacific plate. This time interval is also marked by a global geochemical perturbation of δ13C with a negative excursion at the Aalenian/Bajocian boundary and a positive excursion during the early Bajocian. Evolutionary diversifications of marine invertebrate taxa, namely ammonites, radiolarians, and coccolithophorids, are recorded at that time. Concerning coccolithophorids, this interval witnesses the diversification and expansion of the most successful Mesozoic genus:Watznaueria. In this study, we explore the potential environmental, ecological, and biological forcing at the origin ofWatznaueriadiversification and its effect on the coccolith assemblages through quantification of the absolute and relative abundances of calcareous nannofossils in two Middle Jurassic key sections: Cabo Mondego (Portugal) and Chaudon-Norante (France). In both sections, we find an increase in nannofossil absolute abundance and flux at the beginning of the lower Bajocian, coeval with an increase in absolute and relative abundances ofWatznaueriaspp., followed by a plateau in the middle and upper part of the lower Bajocian. The increase ofWatznaueriaspp. is synchronous with a decrease in relative abundance of other major coccolith taxa, whereas the absolute abundance of these species did not decrease. During the climatically driven early Bajocian eutrophication event,Watznaueriaspp. integrated into the calcareous nannoplankton community in two successive evolutionary steps involving firstW. contractaandW. colaccicchii, and secondW. britannicaandW.aff.manivitiae. Step 1 was driven by an increase in niche carrying capacities linked to the early Bajocian eutrophication. Step 2 was driven by specific adaptation of the newly evolvedWatznaueriaspecies to bloom in nutrient-rich environments not exploited before. These evolutionary events have initiated the 100-Myr reign ofWatznaueriaover the calcareous nannoplankton community.

scholarly journals Analysis of relative abundances on environmental gradients

2018 ◽  
Author(s):  
Fiona Chong ◽  
Matthew Spencer
Keyword(s):  
Compositional Data ◽  
Environmental Gradients ◽  
Compositional Data Analysis ◽  
Depth Gradient ◽  
Negative Numbers ◽  
Marine Communities ◽  
Rates Of Change ◽  
Compositional Approach ◽  
Vertical Slice ◽  
Relative Abundances

Ecologists often analyze relative abundances, which are compositions (sets of non-negative numbers with a fixed sum). However, they have made surprisingly little use of recent advances in the field of compositional data analysis. Compositions form a vector space in which addition and scalar multiplication are replaced by operations known as perturbation and powering. This algebraic structure makes it easy to understand how relative abundances change along environmental gradients. We illustrate this with an analysis of changes in hard-substrate marine communities along a depth gradient. We show how the algebra of compositions can be used to understand patterns in dissimilarity. We use the calculus of simplex-valued functions to estimate rates of change, and to summarize the structure of the community over a vertical slice. We discuss the benefits of the compositional approach in the interpretation and visualization of relative abundance data.

A tale of two peats: characterizing ecosystem-driven differences in chemical composition with depth in natural and drained Finnish mires using Py-GC/MS analytical techniques

2020 ◽  
Author(s):  
Kristy Klein ◽  
Miriam Groβ-Schmölders ◽  
Christine Alewell ◽  
Jens Leifeld
Keyword(s):  
Chemical Composition ◽  
Water Table ◽  
Relative Abundance ◽  
Vascular Plants ◽  
Carbon Sink ◽  
Molecular Biomarkers ◽  
Gas Chromatography Mass Spectrometry ◽  
Driving Mechanism ◽  
Aerobic Decomposition ◽  
Relative Abundances

<p>Intact accumulating peatlands are a globally important terrestrial carbon sink. Climate change and agricultural drainage are degrading these ecosystems, and through increases in aerobic decomposition, shifting their C balance from sink to source. To argue the effectiveness of restoration activities (such as rewetting), techniques are needed that clearly show differences between drained and natural (or drained and rewetted) peatlands. Because these changes are not always macroscopically visible, molecular analysis methods are especially needed to distinguish between ecosystems experiencing net pet growth (sequestering carbon), and those where aerobic decomposition is still a primary driving mechanism. Molecular biomarkers are a useful way to use chemical composition to distinguish these mechanisms.</p><p>This study aimed to compare differences in chemical composition with depth between two peatland sites from a large ombrotrophic mire in Lakkasuo Finland – one natural and one drained. To characterize these chemical shifts, pyrolysis gas chromatography mass spectrometry was used to track changes in relative abundance of various molecular biomarkers and compound classes (ie., aromatics, Sphagnum phenols, lignin, N-containing compounds, n-alkanes, etc.) with depth across both sites. Three replicate cores per site were collected, allowing for statistical evaluation of the relative abundances of these compounds. Using radiocarbon dating at three depths per core, the drained and natural sites were also matched by age for reference purposes. Significant differences were found for the Sphagnum-specific biomarker, p-isopropenylphenol, aromatics, and lignin, to the approximate current depth of the drained peatland water table. Higher phenolic compound class abundance indicated inhibited aerobic decomposition in the natural cores. An increasing trend in lignin biomarker relative abundance with depth was observed in the natural site, despite the identification of comparatively fewer vascular plants during the macroscopic analysis. Rather than a higher abundance of palaeo-ecological vascular plants, this trend is considered to be an indicator of preferential preservation of lignin compounds with anaerobic conditions. Below the depth of the water table, the relative abundances of most biomarkers stabilized, indicating the existance of similar environmental conditions in both sites prior to drainage. These data were compared and are in agreement with findings from elemental analysis (CHNO) and bulk isotopic (<sup>13</sup>C and <sup>15</sup>N) data measured on the same cores. Collectively, these data suggest that observed shifts in chemical composition in the natural and drained cores reflect the effect of different hydrological conditions between the two sites.</p>

scholarly journals Alcov: Estimating Variant of Concern Abundance from SARS-CoV-2 Wastewater Sequencing Data

2021 ◽  
Author(s):  
Isaac Ellmen ◽  
Michael D.J. Lynch ◽  
Delaney Nash ◽  
Jiujun Cheng ◽  
Jozef I. Nissimov ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Data ◽  
Relative Abundance ◽  
Community Level ◽  
Next Generation ◽  
Sequencing Data ◽  
Complete Genomes ◽  
Relative Abundances ◽  
Wastewater Samples ◽  
Generation Sequencing

Detection of SARS-CoV-2 in wastewater is an important strategy for community level surveillance. Variants of concern (VOCs) can be detected in the wastewater samples using next generation sequencing, however it can be challenging to determine the relative abundance of different VOCs since the reads cannot be assembled into complete genomes. Here, we present Alcov (abundance learning of SARS-CoV-2 variants), a tool that uses mutation frequencies in SARS-CoV-2 sequencing data to predict the distribution of VOC lineages in the sample. We used Alcov to predict the distributions of lineages from three wastewater samples which agreed well with clinical data. By predicting not just which VOCs are present, but their relative abundances in the population, Alcov extracts a more complete snapshot of the variants which are circulating in a community.

Sign in / Sign up

Export Citation Format

Share Document