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Ma Y, Liu D, Hua J, Lu W. Dual-energy micro-focus computed tomography based on the energy-angle correlation of inverse Compton scattering source. JOURNAL OF X-RAY SCIENCE AND TECHNOLOGY 2023; 31:1227-1243. [PMID: 37638471 DOI: 10.3233/xst-230093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
BACKGROUND Inverse Compton scattering (ICS) source can produce quasi-monoenergetic micro-focus X-rays ranging from keV to MeV level, with potential applications in the field of high-resolution computed tomography (CT) imaging. ICS source has an energy-angle correlated feature that lower photon energy is obtained at larger emission angle, thus different photon energies are inherently contained in each ICS pulse, which is especially advantageous for dual- or multi-energy CT imaging. OBJECTIVE This study proposes a dual-energy micro-focus CT scheme based on the energy-angle correlation of ICS source and tests its function using numerical simulations. METHODS In this scheme, high- and low-energy regions are chosen over the angular direction of each ICS pulse, and dual-energy projections of the object are obtained by an angularly-splicing scanning method. The field-of-view (FOV) of ICS source is extended simultaneously through this scanning method, thus the scale of the imaging system can be efficiently reduced. A dedicated dual-energy CT algorithm is developed to reconstruct the monoenergetic attenuation coefficients, electron density, and effective atomic number distributions of the object. RESULTS A test object composed of different materials (carbon, aluminium, titanium, iron and copper) and line pairs with different widths (15/24/39/60 μm) is imaged by the proposed dual-energy CT scheme using numerical simulations, and high-fidelity monoenergetic attenuation coefficient, electron density, and effective atomic number distributions are obtained. All the line pairs are well identified, and the contrast ratio of the 15 μm lines is 22%, showing good accordance with the theoretical predictions. CONCLUSIONS The proposed dual-energy CT scheme can reconstruct fine inner structures and material compositions of the object simultaneously, opening a new possibility for the application of ICS source in the field of non-destructive testing.
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Affiliation(s)
- Yue Ma
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
- Department of Engineering Physics, Tsinghua University, Beijing, China
| | - Dexiang Liu
- Department of Engineering Physics, Tsinghua University, Beijing, China
| | - Jianfei Hua
- Department of Engineering Physics, Tsinghua University, Beijing, China
| | - Wei Lu
- Department of Engineering Physics, Tsinghua University, Beijing, China
- Beijing Academy of Quantum Information Sciences, Beijing, China
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Deep-sea infauna with calcified exoskeletons imaged in situ using a new 3D acoustic coring system (A-core-2000). Sci Rep 2022; 12:12101. [PMID: 35896776 PMCID: PMC9329462 DOI: 10.1038/s41598-022-16356-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 07/08/2022] [Indexed: 11/08/2022] Open
Abstract
The deep ocean is Earth’s largest habitable space inhabited by diverse benthic organisms. Infauna play crucial roles in shaping sedimentary structures, relocating organic matter, porewater chemistry, and hence biogeochemical cycles. However, the visualization and quantification of infauna in situ inside deep-sea sediment has been challenging, due to their sparse distribution and that deep-sea cameras do not visualize animals living below the sediment surface. Here, we newly developed a 3D acoustic “coring” system and applied it to visualize and detect burrowing bivalves in deep-sea sediments. The in situ acoustic observation was conducted at a dense colony of vesicomyid clams in a hydrocarbon seep in Sagami Bay, Japan, focusing on a patch of juvenile clams with a completely infaunal life style. We clearly observed strong backscatters from the top and lower edges of animals in our 3D acoustic data. At least 17 reflectors were identified in the survey area (625 cm2), interpreted to correspond to living clams. The estimated depths of the lower edge of clams ranged between 41 and 98 mm. The acoustic system presented here is effective for detecting and monitoring infauna with calcified exoskeletons. This novel tool will help us better assess and understand the distribution of deep-sea infauna, particularly those groups with hard exoskeletons, as well as biogeochemical cycles.
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Wyness AJ, Fortune I, Blight AJ, Browne P, Hartley M, Holden M, Paterson DM. Ecosystem engineers drive differing microbial community composition in intertidal estuarine sediments. PLoS One 2021; 16:e0240952. [PMID: 33606695 PMCID: PMC7895378 DOI: 10.1371/journal.pone.0240952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/23/2021] [Indexed: 01/04/2023] Open
Abstract
Intertidal systems are complex and dynamic environments with many interacting factors influencing biochemical characteristics and microbial communities. One key factor are the actions of resident fauna, many of which are regarded as ecosystem engineers because of their bioturbation, bioirrigation and sediment stabilising activities. The purpose of this investigation was to elucidate the evolutionary implications of the ecosystem engineering process by identifying, if any, aspects that act as selection pressures upon microbial communities. A mesocosm study was performed using the well characterised intertidal ecosystem engineers Corophium volutator, Hediste diversicolor, and microphytobenthos, in addition to manual turbation of sediments to compare effects of bioturbation, bioirrigation and stabilisation. A range of sediment functions and biogeochemical gradients were measured in conjunction with 16S rRNA sequencing and diatom taxonomy, with downstream bacterial metagenome function prediction, to identify selection pressures that incited change to microbial community composition and function. Bacterial communities were predominantly Proteobacteria, with the relative abundance of Bacteroidetes, Alphaproteobacteria and Verrucomicrobia being partially displaced by Deltaproteobacteria, Acidobacteria and Chloroflexi as dissolved oxygen concentration and redox potential decreased. Bacterial community composition was driven strongly by biogeochemistry; surface communities were affected by a combination of sediment functions and overlying water turbidity, and subsurface communities by biogeochemical gradients driven by sediment reworking. Diatom communities were dominated by Nitzschia laevis and Achnanthes sp., and assemblage composition was influenced by overlying water turbidity (manual or biogenic) rather than direct infaunal influences such as grazing.
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Affiliation(s)
- Adam J. Wyness
- Sediment Ecology Research Group, Scottish Oceans Institute, School of Biology, University of St Andrews, East Sands, St Andrews, United Kingdom
- Coastal Research Group, Department of Zoology and Entomology, Rhodes University, Makhanda, South Africa
- * E-mail:
| | - Irene Fortune
- Sediment Ecology Research Group, Scottish Oceans Institute, School of Biology, University of St Andrews, East Sands, St Andrews, United Kingdom
| | - Andrew J. Blight
- Sediment Ecology Research Group, Scottish Oceans Institute, School of Biology, University of St Andrews, East Sands, St Andrews, United Kingdom
| | - Patricia Browne
- Sediment Ecology Research Group, Scottish Oceans Institute, School of Biology, University of St Andrews, East Sands, St Andrews, United Kingdom
| | - Morgan Hartley
- Sediment Ecology Research Group, Scottish Oceans Institute, School of Biology, University of St Andrews, East Sands, St Andrews, United Kingdom
| | - Matthew Holden
- Infection Group, School of Medicine, University of St Andrews, North Haugh, St Andrew, United Kingdom
| | - David M. Paterson
- Sediment Ecology Research Group, Scottish Oceans Institute, School of Biology, University of St Andrews, East Sands, St Andrews, United Kingdom
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Kohzu A, Watanabe H, Imai A, Takaya N, Miura S, Shimotori K, Komatsu K. Magnetic Resonance Imaging as a Novel Method for Elucidating Sediment Burrow Structures and Functions. ACS OMEGA 2020; 5:14933-14941. [PMID: 32637767 PMCID: PMC7330907 DOI: 10.1021/acsomega.8b00192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/29/2020] [Indexed: 06/11/2023]
Abstract
Burrow structures produced by various benthic animals in sediments are important components of aquatic ecosystems, allowing the circulation of interstitial water via ingress of fresh bottom water into the burrows upon feeding and intraburrow migration. Although X-ray computed tomography has been used to visualize burrow structures, it could not reveal the structures in the soft mud in Lake Kasumigaura, where evaluation of the water-circulation effect of burrows is an important issue. Here, we describe the first attempt to use magnetic resonance (MR) imaging (MRI) to visualize intact burrow structures in the soft mud sediment cores collected from a eutrophic lake. Our MRI application clarified the dynamic distribution of burrows inhabited by chironomids in the soft mud that previous studies could not visualize. By examining the relationships between the degree of chloride ion depletion in deeper layers and the burrow density calculated from the MR images, we were able to consistently explain the water-circulation effect of burrows, suggesting the higher reliability of burrow density calculated from MR images. In addition, we were able to evaluate the activity of burrows, which is difficult to achieve in sediment core experiments. We observed a smaller water-circulation effect of burrows on ammonium ions than on chloride ions, suggesting the enhancement of ammonium production or release in burrow-rich sediments.
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Affiliation(s)
- Ayato Kohzu
- Center
for Regional Environmental Research, National
Institute for Environmental Studies, Tsukuba, Ibaraki 305-8506, Japan
| | - Hidehiro Watanabe
- Center
for Environmental Measurement and Analysis, National Institute for Environmental Studies, Tsukuba, Ibaraki 305-8506, Japan
| | - Akio Imai
- Center
for Regional Environmental Research, National
Institute for Environmental Studies, Tsukuba, Ibaraki 305-8506, Japan
| | - Nobuhiro Takaya
- Center
for Environmental Measurement and Analysis, National Institute for Environmental Studies, Tsukuba, Ibaraki 305-8506, Japan
| | - Shingo Miura
- Center
for Regional Environmental Research, National
Institute for Environmental Studies, Tsukuba, Ibaraki 305-8506, Japan
| | - Koichi Shimotori
- Center
for Regional Environmental Research, National
Institute for Environmental Studies, Tsukuba, Ibaraki 305-8506, Japan
| | - Kazuhiro Komatsu
- Center
for Regional Environmental Research, National
Institute for Environmental Studies, Tsukuba, Ibaraki 305-8506, Japan
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Pennafirme S, Machado AS, Machado AC, Lopes RT, Lima ICB, Crapez MAC. Monitoring bioturbation by a small marine polychaete using microcomputed tomography. Micron 2019; 121:77-83. [PMID: 30951928 DOI: 10.1016/j.micron.2019.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/23/2019] [Accepted: 03/23/2019] [Indexed: 01/12/2023]
Abstract
Bioturbation is one of the principle biological processes involved in transporting particles and solutes within sediments, which contributes to the maintenance of biodiversity. In muddy polluted environments, bioturbation may increase pollutant flux at the water-sediment interface, thereby enhancing contaminant bioavailability. The behavior of organisms dictates bioturbation, and gallery shape influences the magnitude of solute transport. Thus, quantitative investigations of gallery shape are fundamental to understanding how pollutant and solute transport is enhanced by bioturbators in muddy sediments. However, there is a lack of tools for quantitatively analyzing gallery geometry, especially for assessing bioturbation and gallery properties through time. Despite the potential of microcomputed tomography (μCT) for quantitative analyses of bioturbation, few such studies have been carried out. Here, we aimed to investigate the potential of μCT for quantitatively assessing the shape and geometric properties of galleries made by small marine polychaetes and their evolution through time in muddy sediments. We focused on Laeonereis acuta (Treadwell, 1923) (Nereididae, Polychaeta), which is a key bioturbator in marine coastal ecosystems. Using 2D and 3D images generated from μCT, we evaluated L. acuta galleries and propose several indexes to quantitatively assess gallery evolution and the role of gallery parameters in bioturbation. Quantitative investigations of polychaete galleries using μCT can assist in monitoring how bioturbation influences sedimentary systems.
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Affiliation(s)
- Simone Pennafirme
- Marine Biology Department, Federal Fluminense University, Niterói, RJ, Brazil; Department of Nuclear Physics, Federal University of Rio de Janeiro, RJ, Brazil.
| | | | | | - Ricardo T Lopes
- Department of Nuclear Physics, Federal University of Rio de Janeiro, RJ, Brazil
| | - Inaya C B Lima
- Department of Nuclear Physics, Federal University of Rio de Janeiro, RJ, Brazil
| | - Mirian A C Crapez
- Marine Biology Department, Federal Fluminense University, Niterói, RJ, Brazil
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Zhang N, Thompson CEL, Townend IH, Rankin KE, Paterson DM, Manning AJ. Nondestructive 3D Imaging and Quantification of Hydrated Biofilm-Sediment Aggregates Using X-ray Microcomputed Tomography. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:13306-13313. [PMID: 30354082 DOI: 10.1021/acs.est.8b03997] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Biofilm-sediment aggregate (BSA) contains a high water content, either within internal pores and channels or bound by extracellular polymeric substances (EPS) forming a highly hydrated biofilm matrix. Desiccation of BSAs alters the biofilm morphology and thus the physical characteristics of porous media, such as the binding matrix within BSA and internal pore geometry. Observing BSAs in their naturally hydrated form is essential but hampered due to the lack of techniques for imaging and discerning hydrated materials. Generally, imagery techniques (scanning electron microscopy (SEM), transmission electron microscopy (TEM), and focused ion beam nanotomography (FIB-nt)) involve the desiccation of BSAs (freeze-drying or acetone dehydration) or prevent differentiation between BSA components such as inorganic particles and pore water (confocal laser scanning microscopic (CLSM)). Here, we propose a novel methodology that simultaneously achieves the 3D visualization and quantification of BSAs and their components in their hydrated form at a submicron resolution using X-ray microcomputed tomography (μ-CT). It enables the high-resolution detection of comparable morphology of multiphase components within a hydrated aggregate: each single inorganic particle and the hydrated biofilm matrix. This allows the estimation of aggregate density and the illustration of biofilm-sediment binding matrix. This information provides valuable insights into investigations of the transport of BSAs and aggregate-associated sediment particles, contaminants (such as microplastics), organic carbon, and their impacts on aquatic biogeochemical cycling.
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Affiliation(s)
- Naiyu Zhang
- School of Ocean and Earth Science , National Oceanography Centre, University of Southampton , Southampton SO14 3ZH , U.K
| | - Charlotte E L Thompson
- School of Ocean and Earth Science , National Oceanography Centre, University of Southampton , Southampton SO14 3ZH , U.K
| | - Ian H Townend
- School of Ocean and Earth Science , National Oceanography Centre, University of Southampton , Southampton SO14 3ZH , U.K
| | - Kathryn E Rankin
- μ-VIS X-ray Imaging Centre, Faculty of Engineering and the Environment, Highfield Campus , University of Southampton , Southampton SO17 1BJ , U.K
| | - David M Paterson
- Sediment Ecology Research Group, Scottish Oceans Institute, School of Biology , University of St. Andrews , St. Andrews KY16 8LB , U.K
| | - Andrew J Manning
- HR Wallingford Ltd., Coasts & Oceans Group, Wallingford OX10 8BA , United Kingdom
- School of Environmental Sciences , University of Hull , Hull HU6 7RX , United Kingdom
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Crespo D, Grilo TF, Baptista J, Coelho JP, Lillebø AI, Cássio F, Fernandes I, Pascoal C, Pardal MÂ, Dolbeth M. New climatic targets against global warming: will the maximum 2 °C temperature rise affect estuarine benthic communities? Sci Rep 2017; 7:3918. [PMID: 28634416 PMCID: PMC5478632 DOI: 10.1038/s41598-017-04309-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/12/2017] [Indexed: 11/09/2022] Open
Abstract
The Paris Agreement signed by 195 countries in 2015 sets out a global action plan to avoid dangerous climate change by limiting global warming to remain below 2 °C. Under that premise, in situ experiments were run to test the effects of 2 °C temperature increase on the benthic communities in a seagrass bed and adjacent bare sediment, from a temperate European estuary. Temperature was artificially increased in situ and diversity and ecosystem functioning components measured after 10 and 30 days. Despite some warmness effects on the analysed components, significant impacts were not verified on macro and microfauna structure, bioturbation or in the fluxes of nutrients. The effect of site/habitat seemed more important than the effects of the warmness, with the seagrass habitat providing more homogenous results and being less impacted by warmness than the adjacent bare sediment. The results reinforce that most ecological responses to global changes are context dependent and that ecosystem stability depends not only on biological diversity but also on the availability of different habitats and niches, highlighting the role of coastal wetlands. In the context of the Paris Agreement it seems that estuarine benthic ecosystems will be able to cope if global warming remains below 2 °C.
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Affiliation(s)
- Daniel Crespo
- Centre for Functional Ecology - CFE, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal.
| | - Tiago Fernandes Grilo
- MARE - Marine and Environmental Sciences Centre, Laboratório Marítimo da Guia - Faculdade de Ciências da Universidade de Lisboa, Av. Nossa Senhora do Cabo, 939, 2750-374, Cascais, Portugal
| | - Joana Baptista
- Centre for Functional Ecology - CFE, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - João Pedro Coelho
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
- Department of Chemistry & CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Ana Isabel Lillebø
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Fernanda Cássio
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Isabel Fernandes
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Cláudia Pascoal
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Miguel Ângelo Pardal
- Centre for Functional Ecology - CFE, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Marina Dolbeth
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
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