Application of Computer-Aided Tomography (Ct) to the Study of Estuarine Benthic Communities

Perez, Kenneth T.; Davey, Earl; Moore, Richard H.; Burn, Peter R.; Rosol, Michael; Cardin, John A.; Johnson, Roxanne; Kopans, Daniel N.

doi:10.1890/1051-0761(1999)009[1050:aocatc]2.0.co;2

Cited by 32 publications

(15 citation statements)

References 21 publications

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“…CT‐scan data were analyzed to quantify belowground biomass in each core over time. CT scans of the sediment cores produce a digital image based on core material density differences (Perez et al, 1999). Calibration rods of known density were inserted into a subset of five cores during the CT scanning (following Davey et al, 2011).…”

Section: Methodsmentioning

confidence: 68%

“…First, using CT scans of sediment cores, we made repeated belowground biomass measurements on the same live plants grown in the greenhouse over the course of the 2013 summer season, which enabled us to tightly correlate belowground production to aboveground reproductive phenology. This approach allowed us to quantify belowground biomass through time without disturbing the growing plants (Perez et al, 1999; Davey et al, 2011). By using this method, we could also more precisely track biomass allocation in the plants, thereby reducing the effect of intramarsh spatial variability associated with destructive field sampling.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Flowering and biomass allocation in U.S. Atlantic coast Spartina alterniflora

Crosby

Ivens‐Duran

Bertness

et al. 2015

American J of Botany

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Section: Methodsmentioning

confidence: 68%

Section: Methodsmentioning

confidence: 99%

Flowering and biomass allocation in U.S. Atlantic coast Spartina alterniflora

Crosby

Ivens‐Duran

Bertness

et al. 2015

American J of Botany

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“…Even if CT-scan use needs improvements as specify below, this approach proved useful in this study, for linking the vertical distributions of biogenic structures and of foraminifera in sediments. Due to the high cost of CT-scans and poor access to this technique for non medical studies, studies based on this technique have tended to involve the scanning of only one core per sampling site Mermillod-Blondin et al, 2003;Michaud et al, 2003;Mazik et al, 2008) or small numbers of replicates (Perez et al, 1999;Rosenberg et al, 2007). For these reasons, we were able to scan only one core per sampling station in this study.…”

Section: Ct-scan To Assess Macrofaunal Bioturbationmentioning

confidence: 99%

“…This technical development has resulted in greater use of CT-scans being made in both marine (e.g. Perez et al, 1999;Mermillod-Blondin et al, 2003;Rosenberg et al, 2007;Mazik et al, 2008;Rosenberg et al, 2008) and terrestrial studies (Daniel et al, 1997). Computed tomography is now recognized to be an efficient tool for the three-dimensional exploration of biogenic structures and accurate volume quantification in soil and sediments.…”

Section: Introductionmentioning

confidence: 99%

Influence of the mode of macrofauna-mediated bioturbation on the vertical distribution of living benthic foraminifera: First insight from axial tomodensitometry

Bouchet

Sauriau

Debenay

et al. 2009

Journal of Experimental Marine Biology and Ecology

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We investigated the influence of bioturbation by macrofauna on the vertical distribution of living (stained) benthic foraminifera in marine intertidal sediments. We investigated the links between macrofaunal bioturbation and foraminiferal distribution, by sampling from stations situated on a gradient of perturbation by oyster-farming, which has a major effect on benthic faunal assemblages. Sediment cores were collected on the French Atlantic coast, from three intertidal stations: an oyster farm, an area without oysters but affected by oyster biodeposits, and a control station. Axial tomodensitometry (CT-scan) was used for three-dimensional visualization and two-dimensional analysis of the cores. Biogenic structure volumes were quantified and compared between cores. We collected the macrofauna, living foraminifera, shells and gravel from the cores after scanning, to validate image analysis. We did not investigate differences in the biogenic structure volume between cores. However, biogenic structure volume is not necessarily proportional to the extent of bioturbation in a core, given that many biodiffusive activities cannot be detected on CT-scans. Biodiffusors and larger gallery-diffusors were abundant in macrofaunal assemblage at the control station. By contrast, macrofaunal assemblages consisted principally of downward-conveyors at the two stations affected by oyster farming. At the control station, the vertical distribution of biogenic structures mainly built by the biodiffusor Scorbicularia plana and the large gallery-diffusor Hediste diversicolor was significantly correlated with the vertical profiles of living foraminifera in the sediment, whereas vertical distributions of foraminifera and downward-conveyors were not correlated at the station affected by oyster farming. This relationship was probably responsible for the collection of foraminifera in deep sediment layers (> 6 cm below the sediment surface) at the control station. As previously suggested for other species, oxygen diffusion may occur via the burrows built by S. plana and H. diversicolor, potentially increasing oxygen penetration and providing a favorable microhabitat for foraminifera in terms of oxygen levels. By contrast, the absence of living foraminifera below 6 cm at the stations affected by oyster farming was probably associated with a lack of biodiffusor and large gallery-diffusor bioturbation. Our findings suggest that the effect of macrofaunal bioturbation on the vertical distribution of foraminiferal assemblages in sediments depends on the effects of the macrofauna on bioirrigation and sediment oxidation, as deduced by Eh values, rather than on the biogenic structure volume produced by macrofauna. The loss of bioturbator functional diversity due to oyster farming may thus indirectly affect infaunal communities by suppressing favorable microhabitats produced by bioturbation.

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“…CT imaging has been used to visualize and quantify differences in the belowground area of tubes and tunnels of benthic animals such as polychaetes, amphipods, burrowing sea anemones, and shrimp among sites along a pollution gradient in Narragansett Bay, Rhode Island, USA (Perez et al 1999). CT imaging has also been used to identify and quantify volumes of worm burrows and other benthic organisms in sediments (Mazik et al 2008, Rosenberg et al 2008, and to determine the effects of hypoxia on burrow construction (Weissberger et al 2009).…”

Section: Introductionmentioning

confidence: 99%

Use of computed tomography imaging for quantifying coarse roots, rhizomes, peat, and particle densities in marsh soils

Davey

Wigand

Johnson

et al. 2011

Ecological Applications

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Computed tomography (CT) imaging has been used to describe and quantify subtidal, benthic animals such as polychaetes, amphipods, and shrimp. Here, for the first time, CT imaging is used to quantify wet mass of coarse roots, rhizomes, and peat in cores collected from organic-rich (Jamaica Bay, New York) and mineral (North Inlet, South Carolina) Spartina alterniflora soils. Image analysis software was coupled with the CT images to measure abundance and diameter of the coarse roots and rhizomes in marsh soils. Previously, examination of marsh roots and rhizomes was limited to various hand-sieving methods that were often time-consuming, tedious, and error prone. CT imaging can discern the coarse roots, rhizomes, and peat based on their varying particle densities. Calibration rods composed of materials with standard densities (i.e., air, water, colloidal silica, and glass) were used to operationally define the specific x-ray attenuations of the coarse roots, rhizomes, and peat in the marsh cores. Significant regression relationships were found between the CT-determined wet mass of the coarse roots and rhizomes and the hand-sieved dry mass of the coarse roots and rhizomes in both the organic-rich and mineral marsh soils. There was also a significant relationship between the soil percentage organic matter and the CT-determined peat particle density among organic-rich and mineral soils. In only the mineral soils, there was a significant relationship between the soil percentage organic matter and the CT-determined peat wet mass. Using CT imaging, significant positive nitrogen fertilization effects on the wet masses of the coarse roots, rhizomes, and peat, and the abundance and diameter of rhizomes were measured in the mineral soils. In contrast, a deteriorating salt marsh island in Jamaica Bay had significantly less mass of coarse roots and rhizomes at depth (10-20 cm), and a significantly lower abundance of roots and rhizomes compared with a stable marsh. However, the diameters of the rhizomes in the deteriorating marsh were significantly greater than in the stable marsh. CT imaging is a rapid approach to quantify coarse roots, rhizomes, peat, and soil particle densities in coastal wetlands, but the method is unable at this time to quantify fine roots.

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Application of Computer-Aided Tomography (Ct) to the Study of Estuarine Benthic Communities

Cited by 32 publications

References 21 publications

Flowering and biomass allocation in U.S. Atlantic coast Spartina alterniflora

Flowering and biomass allocation in U.S. Atlantic coast Spartina alterniflora

Influence of the mode of macrofauna-mediated bioturbation on the vertical distribution of living benthic foraminifera: First insight from axial tomodensitometry

Use of computed tomography imaging for quantifying coarse roots, rhizomes, peat, and particle densities in marsh soils

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