Phantasmal Media

Harrell, D. Fox

doi:10.7551/mitpress/8834.001.0001

Cited by 101 publications

(38 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Where appropriate, statistical tests were corrected for multiple comparisons using the qvalue R package ( 36 ) using a significance threshold of q value < 0.05. Spearman correlation coefficients and associated P values were calculated with the Hmisc R package ( 37 ). Logistic regression models were used to identify which edaphic characteristics predicted the presence of relic DNA (presence is defined as >20% relic DNA).…”

Section: Methodsmentioning

confidence: 99%

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

Carini

Marsden

Leff

et al. 2016

Preprint

View full text Add to dashboard Cite

One Sentence Summary: Soils can harbor substantial amounts of DNA from dead 19 microbial cells; this 'relic' DNA inflates estimates of microbial diversity and obscures 20 assessments of community structure. 21 22 Relic DNA, Carini, et al. 2016 52 However, total microbial DNA can originate from both living and dead cells. Previous 53 work has shown that extracellular DNA and DNA from dead or partially degraded 54 organisms can persist in soils for weeks to years (reviewed in (7-9)). The longevity and 55 size of this extracellular DNA pool is controlled by a myriad of soil factors. For example, 56 complex physical factors such as soil mineralogy, pH and ionic strength control the 57 sorption of DNA to the soil matrix, as well as the molecular integrity of the DNA itself 58 (10, 11). This sorbed DNA can be protected from removal by microbes that use it as a 59 source of transformable genetic material or for nutrition (reviewed in (12)). 61Given the potential for extracellular DNA to persist in soil, we hypothesized that 62 DNA from dead microbes (which we term 'relic DNA') may obscure DNA-based 63 estimates of the diversity and structure of soil microbial communities (13, 14). Such 64 effects should be most apparent if relic DNA is abundant and if the taxa represented in 65 the relic DNA pool are not reflective of the taxa present as living cells. It is important to 66 Relic DNA, Carini, et al. 2016 3 distinguish living microbes from dead microbes because ecological definitions of 67 community-level diversity and structure are meant to encompass organisms actually 68 alive at a site, not both the living and extinct organisms. Here, we used a propidium 69 monoazide (PMA)-based approach (15, 16) to remove relic DNA from a broad range of 70 soil types. We report the amount of microbial DNA derived from relic DNA pools and 71 show how relic DNA affects the observed richness and composition of microbial 72 communities. We also identify which soil characteristics are linked to greater relic DNA 73 effects and discuss the implications of relic DNA on molecular analyses of microbial 74 communities in soil and other environments. 75 76We tested the effect of relic DNA on estimation of microbial diversity by analyzing 77 31 soils collected from a broad range of ecosystem types across the United States, 78 selected to encompass a wide variety of edaphic characteristics ( Supplementary Table 79 S1). Subsamples of each soil were either treated with PMA (n=5) or left untreated (n=5). 80 PMA is a DNA intercalating molecule that is generally excluded by cells with intact 81 membranes, but binds extracellular DNA and DNA of cells with compromised 82 cytoplasmic membranes (15). After exposure to light, intercalated PMA covalently binds 83 and permanently modifies DNA, rendering it un-amplifiable by the polymerase chain 84 reaction (PCR) (15). We used quantitative PCR (qPCR) to calculate the amount of relic 85 DNA by subtracting the number of amplifiable prokaryotic 16S rRNA gene copies or 86 fungal internal transcribe...

show abstract

Section: Methodsmentioning

confidence: 99%

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

Carini

Marsden

Leff

et al. 2016

Preprint

View full text Add to dashboard Cite

show abstract

“…The resulting RPKM expression values were rank-normalized to Van der Waerden (VdW) scores using the formula ( s = Φ −1 ( r / ( n +1))), where s is the VdW score for a gene, r is the rank for that observation, n is the sample size and Φ is the Φ th quantile from the standard normal distribution using tRank in the multic R package (Lunde et al .). Pearson correlation coefficients and P value estimates were calculated for all gene:gene pairs across the VdW-normalized metatranscriptomes and culture experiments (n=10 and 2, respectively) with the rcorr command in the Hmisc R package (Harrell and Dupont). To correct for multiple hypothesis testing, q values were computed from P value estimates using the qvalue R package (Storey and Tibshirani, 2003).…”

Section: Methodsmentioning

confidence: 99%

Patterns of thaumarchaeal gene expression in culture and diverse marine environments

Carini¹,

Dupont²,

Santoro³

2017

Preprint

View full text Add to dashboard Cite

show abstract

“…Relationships between functional genes and bacteria were assessed by Pearson’s correlation coefficient and co-inertia analysis. Correlation tests were performed using the Hmisc package [24] (v.4.1-1). Co-inertia analysis was performed using the made4 package [25].…”

Section: Methodsmentioning

confidence: 99%

Resistome metagenomics from plate to farm: the resistome and microbial composition during food waste feeding and composting on a Vermont poultry farm

Eckstrom

Barlow

2019

Preprint

View full text Add to dashboard Cite

Food waste diversion and composting, either mandated or voluntary, are growing alternatives to traditional waste disposal. An acceptable source of agricultural feed and composting material, methane-emitting food residuals, including post-consumer food scraps, are diverted from landfills allowing recapture of nutrients that would otherwise be lost. However, risk associated with the transfer of antimicrobial resistant bacteria (ARB), antibiotic resistance genes (ARGs), or pathogens from food waste is not well characterized. Using shotgun metagenomic sequencing, ARGs, microbial content, and associated virulence factors were successfully identified across samples from an integrated poultry farm that feeds post-consumer food waste. A total of 495 distinct bacterial species or sub-species, 50 ARGs, and 54 virulence gene sequences were found. ARG sequences related to aminoglycoside, tetracycline, and macrolide resistance were most prominent, while most virulence gene sequences were related to transposon or integron activity. Microbiome content was distinct between on-farm samples and off-farm food waste collection sites, with a reduction in pathogens throughout the composting process. While most samples contained some level of resistance, only 3 resistance gene sequences occurred in both on- and off-farm samples and no multidrug resistance (MDR) gene sequences persisted once on the farm. The risk of incorporating novel or multi-drug resistance from human sources appears to be minimal and the practice of utilizing post-consumer food scraps as feed for poultry and composting material may not present a significant risk for human or animal health. Pearson correlation and co-inertia analysis identified a significant interaction between resistance and virulence genes (P = 0.05, RV = 0.67), indicating that ability to undergo gene transfer may be a better marker for ARG risk than presence of specific bacterial species. This work expands the knowledge of ARG fate during food scrap animal feeding and composting and provides a methodology for reproducible analysis.

show abstract

Phantasmal Media

Cited by 101 publications

References 0 publications

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

Patterns of thaumarchaeal gene expression in culture and diverse marine environments

Resistome metagenomics from plate to farm: the resistome and microbial composition during food waste feeding and composting on a Vermont poultry farm

Contact Info

Product

Resources

About