Recent Advances in Bone Diagenesis

A special issue of Minerals (ISSN 2075-163X). This special issue belongs to the section "Biomineralization and Biominerals".

Deadline for manuscript submissions: 20 September 2024 | Viewed by 7223

Special Issue Editors


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Guest Editor
Harold Hamm School of Geology and Geological Engineering, University of North Dakota, Grand Forks, ND 58202, USA
Interests: vertebrate paleontology; taphonomy; trace element geochemistry; molecular paleontology; paleoecology

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Guest Editor
The Children’s Museum of Indianpolis, 3000 N Meridian St, Indianapolis, IN 46208, USA
Interests: paleopathology; paleohistology; bone chemistry; bone taphonomy and diagenesis

Special Issue Information

Dear Colleagues,

The vertebrate fossil record entices both young and old to learn more about the history of this remarkable planet we share and the Nature of Earth as an active system. Over the last 150 years, studies of vertebrate fossils have advanced our understanding of everything from historical geology to organismal biology, ecologic responses to climate change, and evolution (including our own). Moreover, given their popularity, fossils of vertebrate organisms often form the centerpieces of natural history museum exhibits, where they capture the imagination of current and future scientists on a daily basis. Yet, all of this significance of fossil vertebrates could not exist if their bones, teeth, and scales did not survive the torments of burial and diagenesis.

From the mineralogical perspective, bone is a complex, 3D network of non-stoichiometric hydroxyapatite, while from the biological perspective it is a composite tissue living in dynamic equilibrium. During life, it has the ability to respond to its external environment, constantly shifting and morphing over time in response to physiologic and physical stimuli. However, after death and burial, bone is cast into a mysterious realm of relative obscurity. Microbes attack, groundwaters permeate, isotopes exchange, and bone either surrenders to dissolution or adapts into a transformed version of itself which is attuned to its subterranean environment.

Despite decades of research into how bone fossilization occurs, the processes operating at both visual and submicron scales remain topics of active discussion. Actualistic experiments as well as histologic, elemental, and isotopic studies have each offered clues, but the physicochemical mechanisms which can preserve original crystallites and biomolecules within fossil bones are still ripe for investigation. Paleontologists have traditionally advanced this line of research, but expertise from geochemists, geomicrobiologists, and materials scientists are all needed to fully elucidate the myriad factors at play in bone diagenesis.

In this Special Issue, we highlight recent groundbreaking advances in the study of diagenesis and the fossilization of bones, teeth, and other bioapatitic structures. We hope that this multidisciplinary compendium will spur new interest in this topic and serve as a valuable resource for students and specialists alike. Manuscripts are welcome which discuss topics including, but not limited to:

  1. The transformation of bone from a living tissue to a stable fossil.
  2. Mineralogic transformations occurring during the fossilization of bones and teeth.
  3. Novel applications of trace elements to understanding the diagenetic history of vertebrate fossils.
  4. New analytical approaches to studying the diagenesis of vertebrate remains.
  5. Results of new actualistic experiments concerning bone diagenesis.
  6. Recognition of diagenetic alterations to, and interpretation of, stable isotopic data from fossil bones, teeth, and other bioapatitic structures.
  7. Advances in constraining the types and timings of diagenetic events affecting vertebrate fossils.
  8. Microbial interactions with bone after death and burial.
  9. New insights into comparative taphonomy and diagenesis of bone in natural depositional environments (i.e., taphonomic modes).
  10. The molecular taphonomy of bones and teeth, including controls on biomolecule preservation within such fossils.

Submissions are encouraged from all, especially early-career scientists and researchers who are members of underrepresented communities. We look forward to receiving your submission.

Dr. Paul V. Ullmann
Dr. Jennifer Anné
Guest Editors

Manuscript Submission Information

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Keywords

  • diagenesis
  • vertebrate taphonomy
  • geochemistry
  • stable isotopes
  • molecular paleontology
  • histology

Published Papers (4 papers)

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Research

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15 pages, 7670 KiB  
Article
Controls on Soft Tissue and Cellular Preservation in Late Eocene and Oligocene Vertebrate Fossils from the White River and Arikaree Groups of Nebraska, South Dakota, and Wyoming
by John E. Gallucci, Grace Woolslayer, Kelsey Barker, Brian Kibelstis, Allison R. Tumarkin-Deratzian, Paul V. Ullmann, David E. Grandstaff and Dennis O. Terry, Jr.
Minerals 2024, 14(5), 497; https://doi.org/10.3390/min14050497 - 8 May 2024
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Abstract
Previous studies on microtaphonomy have identified multiple types of organic microstructures in fossil vertebrates from a variety of time periods and past environmental settings. This study investigates potential taphonomic, paleoenvironmental, and paleoclimatic controls on soft tissue and cellular preservation in fossil bone. To [...] Read more.
Previous studies on microtaphonomy have identified multiple types of organic microstructures in fossil vertebrates from a variety of time periods and past environmental settings. This study investigates potential taphonomic, paleoenvironmental, and paleoclimatic controls on soft tissue and cellular preservation in fossil bone. To this end, fifteen vertebrate fossils were studied: eight fossils collected from the Oligocene Sharps Formation of the Arikaree Group in Badlands National Park, South Dakota, and seven fossils from formations in the underlying White River Group, including the Oligocene Brule Formation of Badlands National Park, and the Eocene Chadron Formation of Flagstaff Rim, Wyoming; Toadstool Geologic Park, Nebraska; and Badlands National Park, South Dakota. A portion of each fossil was demineralized to identify any organic microstructures preserved within the fossils. We investigated several factors which may have influenced cellular/soft tissue decay and/or preservation pathways, including taxonomic identity, paleoclimatic conditions, depositional environment, and general diagenetic history (as interpreted through thin section analysis). Soft tissue microstructures were preserved in all fossil samples, and cellular structures morphologically consistent with osteocytes were recovered from 11 of the 15 fossil specimens. Preservation of these microstructures was found to be independent of taxonomy, paleoclimate regime, apatite crystallinity, depositional environment, and general diagenetic history, indicating that biogeochemical reactions operating within microenvironments within skeletal tissues, such as within individual osteocyte lacunae or Haversian canals, may exert stronger controls on soft tissue and biomolecular decay or stabilization than external environmental (or climatic) conditions. Full article
(This article belongs to the Special Issue Recent Advances in Bone Diagenesis)
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19 pages, 3373 KiB  
Article
Characterization of Diagenetiforms in an Expanded Proteome of the Extinct Moa (Dinornithidae): Identifying Biological, Diagenetic, Experimental Artifact, and Mislabeled Modifications in Degraded Tissues
by Elena R. Schroeter
Minerals 2024, 14(2), 137; https://doi.org/10.3390/min14020137 - 26 Jan 2024
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Abstract
Proteomic analyses of extinct moa (Dinornithidae; ~800–1000 years) bone tissue previously revealed preserved collagens (I, II, and V), as well as several biological post-translational modifications (PTMs) and diagenetic peptide sequence alterations. The diagenetiforms detected in that study provided a baseline of PTM preservation [...] Read more.
Proteomic analyses of extinct moa (Dinornithidae; ~800–1000 years) bone tissue previously revealed preserved collagens (I, II, and V), as well as several biological post-translational modifications (PTMs) and diagenetic peptide sequence alterations. The diagenetiforms detected in that study provided a baseline of PTM preservation in degraded tissues, identifying sequence alterations that could be accounted for in bioinformatic data searches (e.g., carboxymethyllysine). Subsequently, an improved extraction and sample preparation methodology, coupled with higher resolution mass spectrometry analyses, identified a wealth of previously unidentified non-collagenous proteins (NCPs) from the specimen. Here, in-depth analyses of the PTMs preserved in the expanded data set provide a detailed look at the types of PTMs (i.e., biological, diagenetic, and potential experimental artifacts) that occur in degraded tissues, the proteins they occur on, and the amino acids they modify. In total, 10 biological PTMs (e.g., ubiquitylation) and 18 diagenetic PTMs, including two advanced glycation end products (e.g., dihydroxy methylglyoxal adduction) and 12 types of oxidative damage (e.g., pyrrolidone formation from proline), were detected. In addition, peptides displaying diagenetic backbone cleavage (hydrolysis) were frequently observed to possess unidentified, variable mass shifts at their broken terminus, which search software would attempt to erroneously identify as different PTMs. The modifications characterized in the bones of this specimen, both in collagens and in NCPs, provide insight into patterns of preservation and degradation that paleoproteomic studies can utilize when searching and interpreting data sets from fossil tissue. Full article
(This article belongs to the Special Issue Recent Advances in Bone Diagenesis)
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25 pages, 9505 KiB  
Article
Actualistic Testing of the Influence of Groundwater Chemistry on Degradation of Collagen I in Bone
by Paul V. Ullmann, Kristyn K. Voegele and Kenneth J. Lacovara
Minerals 2023, 13(5), 596; https://doi.org/10.3390/min13050596 - 25 Apr 2023
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Abstract
Recent experiments have heightened our understanding of reactions which can stabilize biomolecules during early diagenesis, yet little remains known about how groundwater chemistry can aid or hinder molecular preservation within a bone through geologic time. To elucidate this issue, we conducted actualistic experiments [...] Read more.
Recent experiments have heightened our understanding of reactions which can stabilize biomolecules during early diagenesis, yet little remains known about how groundwater chemistry can aid or hinder molecular preservation within a bone through geologic time. To elucidate this issue, we conducted actualistic experiments of bone decay employing varied fluid compositions to simulate a suite of groundwaters. Modern domestic chicken (Gallus gallus) femora were placed in a matrix of compositionally- and texturally-mature, fluvially-deposited sand. To simulate groundwater flow, deionized water or solutions enriched in calcium carbonate, phosphate, or iron were percolated through separate trials for a period of 90 days. After completion of the experiment, degradation of the bones was examined via histologic thin sectioning and two immunoassays against collagen I, the primary bone structural protein: immunofluorescence and enzyme-linked immunosorbent assay. Collagen loss was found to be greatest in the iron trial and least in the calcium carbonate trial, the latter of which experienced partial permineralization with calcite over the course of the experiment. Specifically, the iron trial was found to retain only ~35 ng of collagen I per 100 ng of protein extract, whereas the calcium carbonate trial retained ~90 ng of collagen I. Further, in the iron and calcium carbonate trials, cementation of sediment onto bone surfaces preferentially occurred over more porous regions of the epiphyses, perhaps stimulated by greater release of decay compounds from these regions of the bones. Of the two trials exhibiting intermediate results, the phosphate trial induced slightly greater decay of collagen than the deionized water control, which retained ~60 ng and ~80 ng of collagen I per 100 ng of protein extract, respectively. These results demonstrate that highly acidic conditions during early diagenesis can overwhelm any preservative effects of free radical-mediated stabilization reactions, whereas early-diagenetic permineralization can drastically slow biomolecular decay (ostensibly by hampering microbial access to the interior of a bone), thereby increasing the likelihood of a bone to retain biomolecules and/or their decay products through protracted diagenesis. Future variations of this actualistic experiment employing varied durations, solute concentrations, bacterial communities, pH values, and/or host sediments could provide further important insights into the ways in which early-diagenetic environments control the initial decay of biomolecules within bone and other tissues. Full article
(This article belongs to the Special Issue Recent Advances in Bone Diagenesis)
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Review

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23 pages, 3233 KiB  
Review
Porphyrin-Based Molecules in the Fossil Record Shed Light on the Evolution of Life
by Juan D. Ayala, Elena R. Schroeter and Mary H. Schweitzer
Minerals 2024, 14(2), 201; https://doi.org/10.3390/min14020201 - 16 Feb 2024
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Abstract
The fossil record demonstrates the preservation of porphyrins (e.g., heme) in organic sediments and the fossilized remains of animals. These molecules are essential components in modern metabolic processes, such as electron transport (cytochromes) and oxygen transport (hemoglobin), and likely originated before the emergence [...] Read more.
The fossil record demonstrates the preservation of porphyrins (e.g., heme) in organic sediments and the fossilized remains of animals. These molecules are essential components in modern metabolic processes, such as electron transport (cytochromes) and oxygen transport (hemoglobin), and likely originated before the emergence of life. The integration and adaptation of porphyrins and structurally similar molecules (e.g., chlorophylls) are key aspects in the evolution of energy production (i.e., aerobic respiration and photosynthesis) and complex life (i.e., eukaryotes and multicellularity). Here, we discuss the evolution and functional diversity of heme-bound hemoglobin proteins in vertebrates, along with the preservation of these molecules in the fossil record. By elucidating the pivotal role of these molecules in the evolution of life, this review lays the groundwork necessary to explore hemoglobin as a means to investigate the paleobiology of extinct taxa, including non-avian dinosaurs. Full article
(This article belongs to the Special Issue Recent Advances in Bone Diagenesis)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

  1. Jasmina Wiemann, Yale University
  2. Ioannis Kontopoulos, University of Copenhagen
  3. John Ejnik, University of Wisconsin-Waterfall
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