A new method for three‐dimensional visualization and quantification of biogenic structures in aquatic sediments using axial tomodensitometry

Abstract

Biogenic structures formed by the activity of macro-and meiobenthic organisms exert a great influence on the physical, chemical, and biological properties of sediments. Although bioturbation processes are recognized as ecologically important, the characterization and quantification of biogenic structures produced by benthic organisms remain difficult. Several techniques (e.g., resin casting, X-radiography) were previously used to quantify these structures. However, due to a lack of definition, entire burrows, including fine structures created by meiobenthic and small macrobenthic species, could not be identified with precision. Here, we show how axial tomodensitometry (CT scan) can be used to visualize biogenic structures and organic matter in three dimensions with high resolution. Further, a simple method for calculating the space occupied by biogenic structures at given depths is developed, based on comparisons of the densities of biogenic structures with those of surrounding sediments. Other potential uses of the CT scan technique in studying benthic ecology are discussed.

Environmental Constraints on the Mechanics of Crawling and Burrowing Using Hydrostatic Skeletons

“…The mechanism by which a crack becomes a cylindrical burrow is not known, but is an important area for future research. Permanent burrows are clearly present and abundant in sediments [47,48], but whether burrowers can move through sediments without leaving a permanent trace is, quite literally, unclear. It is also important to note that both the elastic modulus, E, and fracture toughness, G c , increase with depth in the sediment due to compaction, and that grain size (and therefore cohesion) has a strong effect on both properties, but more research on the depth-dependence of these properties is needed [49].…”

3D visualization and quantification of marine benthic biogenic structures and particle transport utilizing computer-aided tomography

“…Since the pioneering work by Perez et al (1999), the use of CT for analyzing biogenic structures in marine sediments have been used in several Canadian studies (Mermillod-Blondin et al 2003, Dufour et al 2005. In these studies (op.…”

“…Thus, this simplified analysis did not separate structures connected to the sediment surface from those that were not connected, and the analytical technique did not include the biovolume of animals living within shells or dense worm tubes. Although the method was improved in the latter study to obtain a better and quicker analysis, it is not clear how accurate the assessments were because most of the water within the cores had leaked out before scanning (Dufour et al 2005). Another technique used to analyse biogenic structures in sediment was to slice sediment in thin sections and to digitally analyse each section for structures such as burrows, tubes and shells (Rosenberg & Ringdahl 2005).…”

“…The CT technique was initially used in the marine field in a pollution gradient study in Rhode Island, USA (Perez et al 1999). Scientists in Canada later used this technique to estimate the space occupied by biogenic structures by depth in sediment from some different areas (Mermillod-Blondin et al 2003, Dufour et al 2005. Recently a more detailed examination of the sediment from Swedish fjords was done using CT where, for example, the occupied space of recent and relic worm tubes and mollusk shells were visualized and quantified ).…”

Oxygen microprofile in the prepared sediments and its implication for the sediment oxygen consuming process in a heavily polluted river of China

“…In sediments, bioturbation (i.e., the diffusion-like transport caused by fauna activity) will influence the overall transport of DO (Aller 1980). Benthic organisms can construct complex structures in the sediment column and form sediment pores with various shapes and sizes that may or may not be permanent (Dufour et al 2005). These structures may be actively ventilated by their inhabitants and thus possess higher DO levels (Aller and Aller 1998;Kristensen 1983).…”