Computed Tomography: Application in Studying Biogenic Structures in Sediment Cores

Palaios ◽  
1994 ◽  
Vol 9 (1) ◽  
pp. 116 ◽  
Author(s):  
Shaoping Fu ◽  
Friedrich Werner ◽  
Joachim Brossmann
Keyword(s):  
Computed Tomography ◽  
Sediment Cores ◽  
Biogenic Structures

scholarly journals Bioturbational structures in the North Atlantic: new approaches for studying cores

1992 ◽  
Vol 6 ◽  
pp. 106-106
Author(s):  
Shaoping Fu ◽  
Friedrich Werner
Keyword(s):  
North Atlantic ◽  
Sediment Cores ◽  
Three Dimensional ◽  
Bedding Plane ◽  
Lateral Migration ◽  
Core Diameter ◽  
The North ◽  
Biogenic Structures ◽  
Sediment Cover ◽  
The North Atlantic

General environmental correlation, established for trace fossils, is hard to apply to modern sediment cores, for which environmental factors can be measured directly - at least with regard to the top layers. Reasons for this difficulty are obvious: (1) Outcrop volume is limited by the core diameter. (2) Biogenic structures are hard to see, because they have not yet been “developed” by diagenetic processes. (3) Cores are traditionally studied in vertical cuts, in which search patterns parallel to bedding plane - typical for deep-sea environment - are poorly expressed. Therefore cores from the North Atlantic were studied not only by traditional X-ray radiography (both vertical and horizontal cuts), but by computer tomography (CT), which renders series of sections parallel to the bedding plane, as well as a three-dimensional picture, without destroying the valuable core.On the Iceland-Faeroe Ridge, the distribution of ichnocoenoses appears to be largely controlled by microenvironments in connection with local channel systems and their lateral migration. In a local, ridge-parallel channel system at the southern slope, a core from the NE flank shows a vertical alternation of Zoophycos, Trichichnus, and Planolites communities correlating with fluctuations of CaCO3 and the fraction >63μm. In contrast to this, on the opposite slope, sediments are uniform and dominated by Scolicia. On the colder N slope of the ridge, topography is more uniform and the water motion is sluggish. The characteristic and dominant ichnogenus is Chondrites. On top of the ridge the sediment cover becomes very thin, contains large amounts of dropstones, but still Chondrites is dominant.

scholarly journals Biogenic structures in the Arctic: an ecosystem functioning hotspot?

2018 ◽  
Author(s):  
Marie Pierrejean ◽  
Philippe Archambault ◽  
Barbara Neves ◽  
Evan Edinger ◽  
Christian Nozais
Keyword(s):  
Ecosystem Functioning ◽  
Cold Water ◽  
Sediment Cores ◽  
Three Dimensional ◽  
Ammonium Phosphate ◽  
The Arctic ◽  
Benthic Fluxes ◽  
Bare Sediment ◽  
Biogenic Structures ◽  
Associated Species

In deep-sea environments, resources availability and habitat complexity drive the distribution of benthic organisms. Biogenic structures such as cold-water corals and sponges create a three-dimensional habitat that facilitate sediment and resources accumulation and therefore show a high abundance of the associated species compared to bare sediments. However, the functions of these biodiversity hotspots in the ecosystem functioning are still poorly known. In this study, we addressed three main questions: 1) do benthic fluxes vary according to their position within patches and bare sediment? 2) are infaunal communities similar in biogenic structure and bare sediment patches? and finally, 3) which variables explain benthic fluxes in these patches? Infaunal communities and benthic fluxes were examined in Arctic regions presenting two types of biogenic structures: corals (Keratoisis sp.) and arborescent sponges. To compare ecosystem functioning between the biogenic structure versus bare sediment patches, sediment cores were collected to quantify benthic fluxes (nitrate, nitrite, ammonium, phosphate and silicate) and the diversity, abundance and composition of infauna. Multivariate analyses suggested that biogenic structure and bare sediment patches exhibited different infaunal assemblage and a spatial pattern for the benthic fluxes even with a distance of 100 m between the type of patches.

scholarly journals Biogenic structures in the Arctic: an ecosystem functioning hotspot?

2018 ◽  
Author(s):  
Marie Pierrejean ◽  
Philippe Archambault ◽  
Barbara Neves ◽  
Evan Edinger ◽  
Christian Nozais
Keyword(s):  
Ecosystem Functioning ◽  
Cold Water ◽  
Sediment Cores ◽  
Three Dimensional ◽  
Ammonium Phosphate ◽  
The Arctic ◽  
Benthic Fluxes ◽  
Bare Sediment ◽  
Biogenic Structures ◽  
Associated Species

In deep-sea environments, resources availability and habitat complexity drive the distribution of benthic organisms. Biogenic structures such as cold-water corals and sponges create a three-dimensional habitat that facilitate sediment and resources accumulation and therefore show a high abundance of the associated species compared to bare sediments. However, the functions of these biodiversity hotspots in the ecosystem functioning are still poorly known. In this study, we addressed three main questions: 1) do benthic fluxes vary according to their position within patches and bare sediment? 2) are infaunal communities similar in biogenic structure and bare sediment patches? and finally, 3) which variables explain benthic fluxes in these patches? Infaunal communities and benthic fluxes were examined in Arctic regions presenting two types of biogenic structures: corals (Keratoisis sp.) and arborescent sponges. To compare ecosystem functioning between the biogenic structure versus bare sediment patches, sediment cores were collected to quantify benthic fluxes (nitrate, nitrite, ammonium, phosphate and silicate) and the diversity, abundance and composition of infauna. Multivariate analyses suggested that biogenic structure and bare sediment patches exhibited different infaunal assemblage and a spatial pattern for the benthic fluxes even with a distance of 100 m between the type of patches.

scholarly journals Microbial Community Characteristics Largely Unaffected by X-Ray Computed Tomography of Sediment Cores

2021 ◽  
Vol 12 ◽  
Author(s):  
Erica Ewton ◽  
Scott Klasek ◽  
Erin Peck ◽  
Jason Wiest ◽  
Frederick Colwell
Keyword(s):  
Computed Tomography ◽  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Sediment Cores ◽  
Microbial Community Composition ◽  
Ct Scanning ◽  
X Rays ◽  
X Ray ◽  
X Ray Computed

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.

Spatial distribution of Alitta virens burrows in intertidal sediments studied by axial tomodensitometry

2013 ◽  
Vol 93 (6) ◽  
pp. 1543-1552 ◽  
Author(s):  
Flora Salvo ◽  
Suzanne C. Dufour ◽  
Philippe Archambault ◽  
Georges Stora ◽  
Gaston Desrosiers
Keyword(s):  
Organic Matter ◽  
Spatial Distribution ◽  
Ct Scan ◽  
Sediment Cores ◽  
Organic Matter Content ◽  
Matter Content ◽  
Small Scale ◽  
Lawrence Estuary ◽  
Biogenic Structures ◽  
Sheltered Site

Relationships between sediment characteristics and the spatial organization of biogenic structures remain poorly understood, albeit important for characterizing bioturbation impacts and small-scale ecological patterns. Using axial tomodensitometry (CT-scan) and core sectioning, we studied the spatial distribution of Alitta virens burrows in sediment cores from two mudflats with different degrees of exposure along the St Lawrence Estuary, Canada. A variety of burrow morphologies was observed at both sites, with most being I-shaped. Most values measured (organic matter content, mean tomographic intensity, the number and diameter of burrow shafts and the percentage of space they occupy per transverse section) covaried with depth. The more sheltered site had higher organic matter and mud contents, and lower average tomographic intensity values. The spatial distribution of burrow shafts also differed between sites, with the more sheltered site having a higher number of burrow shafts and percentage of biogenic space in the upper sediment column, as well as a greater volume of biogenic structures that were connected to the surface (although intra-site variability was great). Along the horizontal plane and at various depths within sediments, burrow shafts were more randomly distributed at the exposed site, compared to a more even, maximal spacing at the sheltered site. In addition to finding differences in burrow organization at two spatial scales, we found significant correlations between tomographic intensity and (1) the number of burrow shafts, (2) biogenic space and (3) organic matter content. CT-scan data, including tomographic intensity, are useful for examining and comparing biogenic structures in sediment cores.

Dynamics of biotic and abiotic markers of the Anthropocene at Jasper Ridge Biological Preserve, California, USA

2021 ◽  
Author(s):  
M. Allison Stegner ◽  
SeanPaul La Selle ◽  
Brian Sherrod ◽  
Anthony Barnosky ◽  
Elizabeth Hadly
Keyword(s):  
Computed Tomography ◽  
Algal Blooms ◽  
Human Impacts ◽  
Anthropogenic Impacts ◽  
Sediment Cores ◽  
Dry Season ◽  
Global Changes ◽  
Sedimentation Rates ◽  
Low Density ◽  
The 1950S

<p>Human activities changed our planet over the course of the Holocene, but the scale of impacts increased dramatically around the mid-20<sup>th</sup> century, representing the start of the Anthropocene. These pervasive anthropogenic impacts, including pollution, road-building, the rise of plastics, etc., are comparable in magnitude, uniqueness, and geologic perseverance to global changes that mark previous major geologic time intervals. To identify the preservable global and local signals that might be used to characterize the Anthropocene, we examine sediment cores from Searsville Reservoir, a 129-year-old reservoir located in the eastern foothills of the San Francisco Peninsula. We collected eight sediment cores ranging from 7.4 to 8.5 meters in length that appear to have bottomed out on the pre-reservoir surface, indicating average sedimentation rates of 6 to 7 cm per year. This exceptionally high sedimentation rate allows us to explore the Anthropocene geologic record on a sub-annual scale.</p><p>Our analyses to date include sedimentary DNA (sedDNA), pollen, computed tomography (CT) scanning, Carbon and Nitrogen isotopes, radionuclides, Mercury, and X-ray fluorescence (XRF). We find a strong relationship between sediment type and both sedDNA and pollen frequency: sedDNA and pollen are more abundant in the thin, low-density units that are thought to be associated with lower sedimentation rates and high organic inputs during the dry season. SedDNA analyses successfully identified a diversity of insects and vertebrates to the species level, including invasive fish and mosquitos. Computed tomography scans of the cores revealed >300 distinct layers ranging in thickness from <1mm to ~30mm. Many of the thicker laminae show upward-fining, indicative of individual storm events. Sediment density generally decreases from the bottom to the top of the cores, consistent with both sediment compaction and increasing organic inputs as the reservoir filled with sediment and eutrophied. δ<sup>15</sup>N declined over the record, reflecting global δ<sup>15</sup>N depletion due to fossil fuel combustion and artificial nitrogen fertilization for agriculture. δ<sup>13</sup>C was fairly stable prior to around 1950, then became highly variable, possibly related to changes in aquatic productivity (algal blooms) that began in the 1950s. A sharp and well-defined peak in <sup>137</sup>Cs provides evidence of nuclear testing in the 1950s and ‘60s, and serves as a secure chronological tie point for the year 1963. The <sup>137</sup>Cs peak correlates well with the chronology estimated by counting back suspected annual couplets of high density (wet season)/low density (dry-season) sediments. Our analyses reveal a complex interplay between local and global human impacts at Searsville Reservoir, and document the onset of the Anthropocene epoch at fine scale. Searsville is particularly appropriate as a candidate Global Boundary Stratotype Section and Point for the Anthropocene not just because of the unique and highly resolved nature of the sediments, but because the record itself is a direct consequence of human activity—the emplacement of a dam.</p>

scholarly journals Core-CT:  A MATLAB application for the quantitative analysis of sediment and coral cores from X-ray computed tomography (CT) 

2021 ◽  
Author(s):  
Yu Ting Yan ◽  
Stephen Chua ◽  
Thomas DeCarlo ◽  
Philipp Kempf ◽  
Kyle Morgan ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Linear Extension ◽  
Sediment Cores ◽  
Sedimentary Facies ◽  
Ct Number ◽  
Detailed Measurement ◽  
X Ray ◽  
3D Visualisation ◽  
Growth Bands ◽  
X Ray Computed

<div> <p>X-ray computed tomography (CT) is a non-destructive imaging technique that provides three-dimensional (3D) visualisation and high-resolution quantitative data in the form of CT numbers. CT numbers are derived as a function of the X-ray energy, effective atomic number and density of the sample. The sensitivity of the CT number to changes in material density allows it to successfully identify facies changes within sediment cores by detecting downcore shifts in sediment properties, and quantify skeletal linear extension rates and the volume of internal voids from biological erosion of coral cores. Here we present two algorithms to analyse CT scan images specific to geoscience research packaged within an open source MATLAB application (Core-CT). The first algorithm facilitates the computation of representative CT numbers from a user-defined region of interest to identify boundaries of density change (e.g. sedimentary facies, laminations, coral growth bands). The second algorithm enables the segmentation of regions with major density contrast (e.g. internal void space or biogenic material) and the geometric measurements of these irregularities. The versatility of Core-CT for geoscience applications is then demonstrated by utilising CT scans from a range of environmental settings comprising both sediment (Lake Huelde, Chile and Kallang River Basin, Singapore) and coral cores (Thuwal region of Red Sea, Saudi Arabia). Analysis of sediment cores show the capabilities of Core-CT to: 1) locate tsunami deposits from lacustrine sediments, 2) provide rapid and detailed measurement of varved sediments, and 3) identify sedimentary facies from an unsplit shallow marine sediment core. Analysis of coral cores allow us to successfully measure skeletal linear extension from annual growth bands, and provide volumetric quantification and 3D visualisation of internal bioerosion. Core-CT is an accessible, multi-use MATLAB based program that is freely available at GitHub  (https://github.com/yuting-yan/Core-CT).</p> </div><p> </p>

Semi-automated quantification of Ice Rafted Debris in sediment archives with Computed Tomography.

2021 ◽  
Author(s):  
Jan Magne Cederstrøm ◽  
Sunniva Rutledal ◽  
Eivind W. N. Støren ◽  
Willem G. M. van der Bilt
Keyword(s):  
Computed Tomography ◽  
Spatial Resolution ◽  
Marine Sediment ◽  
Sediment Cores ◽  
Ice Sheets ◽  
P Value ◽  
Laboratory Procedure ◽  
Spatial Coverage ◽  
The Impact ◽  
Non Destructive

<p>Ice rafted debris (IRD) in marine sedimentary sequences provide critical information about the evolution of ice sheets. These include enigmatic phases of ice sheet instability like Heinrich events, Dansgaard-Oeschger cycles or Bond events. Higher sampling resolution and greater spatial coverage in IRD records can help gain a better understanding of paleoaclimate, and help predict the future behavior of ice sheets. However, creating high-resolution IRD-records from marine sediment cores is a manual time- and labor-intensive laboratory procedure. By allowing for rapid and non-destructive quantification of micrometer (µm) scale particles, Computed Tomography (CT) holds the potential to increase both resolution and the pace of analysis. We demonstrate the potential of this approach with results from both experimental results and application on conventionally analyzed records. By using basic image processing tools on CT-imagery of phantom-boxes (replicating marine sediment cores with IRD) we counted sand-particles (>150 µm) of different mineralogies ranging from 25-2000 particles/g. The CT-results proved to match the manual counts with a r<sup>2 </sup>of up to 0.99 and a P-value of 0.00. Further, when applying the method on segments of natural marine sediment cores with published IRD-records, we were able to reconstruct the same trends as continuous counts with a 5 times higher spatial resolution. In addition, this non-destructive method gave further information on the impact of bioturbation, grainsize distribution and the sedimentary structure of IRD-deposits. In conclusion, this work can help the field to gain an even better understanding of the behavior of ice sheets by optimizing the efficiency and spatial resolution of IRD-records, while at the same time gaining a better understanding on the processes affecting the IRD-deposits.</p>

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