| Literature DB >> 33912140 |
Erica Ewton1, Scott Klasek1, Erin Peck2, Jason Wiest3, Frederick Colwell2.
Abstract
X-ray computed tomography (CT) scanning is used to study the physical characteristics of soil and sediment cores, allowing scientists to analyze stratigraphy without destroying core integrity. Microbiologists often work with geologists to understand the microbial properties in such cores; however, we do not know whether CT scanning alters microbial DNA such that DNA sequencing, a common method of community characterization, changes as a result of X-ray exposure. Our objective was to determine whether CT scanning affects the estimates of the composition of microbial communities that exist in cores. Sediment cores were extracted from a salt marsh and then submitted for CT scanning. We observed a minimal effect of CT scanning on microbial community composition in the sediment cores either when the cores were examined shortly after recovery from the field or after the cores had been stored for several weeks. In contrast, properties such as sediment layer and marsh location did affect microbial community structure. While we observed that CT scanning did not alter microbial community composition as a whole, we identified a few amplicon sequence variants (13 out of 7,037) that showed differential abundance patterns between scanned and unscanned samples among paired sample sets. Our overall conclusion is that the CT-scanning conditions typically used to obtain images for geological core characterization do not significantly alter microbial community structure. We stress that minimizing core exposure to X-rays is important if cores are to be studied for biological properties. Future investigations might consider variables, such as the length and energy of radiation exposure, the volume of the core, or the degree, to which microbial communities are stressed as important factors in assessing the impact of X-rays on microbes in geological cores.Entities:
Keywords: biomarker; computed tomography scanning; geological cores; microbial communities; sediment; storage
Year: 2021 PMID: 33912140 PMCID: PMC8072469 DOI: 10.3389/fmicb.2021.584676
Source DB: PubMed Journal: Front Microbiol ISSN: 1664-302X Impact factor: 5.640
Figure 1Sediment microbial community structure does not vary as an effect of CT-scanning, but varies between coring sites and layers within the sediment column. (A) displays all communities analyzed in this study, while (B,C) show those from North and South sites, respectively. All panels are Principal Coordinate Analysis (PCoA) ordinations of weighted Unifrac distances calculated from Cumulative Sum Scaling-transformed read counts, with each axis showing its contribution to the variation among communities analyzed.
Figure 2Community composition barplots showing the 10 most abundant classes (all within Bacteria) within all samples analyzed, sectioned by site (North and South) and CT-scanning treatment. These classes contain 68.4% of reads within the dataset. Samples are ordered by increasing depth, and then by storage time.
Figure 3Differentially abundant ASVs across all 22 sets of paired scanned/unscanned samples. Mean percent abundances of these 13 ASVs across each treatment are plotted and colored according to their phylum. Labels, where present, show the most specific taxonomic category or clade to which each ASV belongs.