Role of Sediment Size and Biostratinomy on the Development of Biofilms in Recent Avian Vertebrate Remains

Abstract

Microscopic soft tissues have been identified in fossil vertebrate remains collected from various lithologies. However, the diagenetic mechanisms to preserve such tissues have remained elusive. While previous studies have described infiltration of biofilms in Haversian and Volkmann's canals, biostratinomic alteration (e.g., trampling), and iron derived from hemoglobin as playing roles in the preservation processes, the influence of sediment texture has not previously been investigated. This study uses a Kolmogorov Smirnov Goodness-of-Fit test to explore the influence of biostratinomic variability and burial media against the infiltration of biofilms in bone samples. Controlled columns of sediment with bone samples were used to simulate burial and subsequent groundwater flow. Sediments used in this study include clay-, silt-, and sand-sized particles modeled after various fluvial facies commonly associated with fossil vertebrates. Extant limb bone samples obtained from Gallus gallus domesticus (Domestic Chicken) buried in clay-rich sediment exhibit heavy biofilm infiltration, while bones buried in sands and silts exhibit moderate levels. Crushed bones exhibit significantly lower biofilm infiltration than whole bone samples. Strong interactions between biostratinomic alteration and sediment size are also identified with respect to biofilm development. Sediments modeling crevasse splay deposits exhibit considerable variability; whole-bone crevasse splay samples exhibit higher frequencies of high-level biofilm infiltration, and crushed-bone samples in modeled crevasse splay deposits display relatively high frequencies of low-level biofilm infiltration. These results suggest that sediment size, depositional setting, and biostratinomic condition play key roles in biofilm infiltration in vertebrate remains, and may influence soft tissue preservation in fossil vertebrates.

Actualistic Testing of the Influence of Groundwater Chemistry on Degradation of Collagen I in Bone

“…For example, it would be intriguing to test whether the use of less porous and less permeable sediments (i.e., with a high fraction of clays) within this type of experiment might induce greater decay of collagen within bone due to the constrainment of decay fluids and microbes to within and around decaying remains (cf. [45]). Similarly, it would be intriguing to see if the use of more compositionally-immature sediments (i.e., a feldspathic litharenitic sand) induces greater decay as a result of the production of acidic conditions from gradual dissolution of feldspars and mafic grains.…”

“…We present results of a novel actualistic experiment conducted to explore the influence of groundwater chemistry on protein decay. Building on the methods developed by Carpenter [38], Daniel and Chin [39], and Peterson et al [45], bones were placed within a sedimentary matrix and exposed to a simulated groundwater for a period of 90 days. Our simulated groundwater solutions included calcium carbonate supersaturation, enrichment in dissolved phosphate, and enrichment in ferric iron, along with a deionized water control.…”

Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America

“…On the one hand, endogenous organics including soft tissues inside the bone could be rapidly decomposed by intensive metabolic activity of microorganisms after the death of vertebrates [20]. On the other hand, other taphonomic studies have shown that, in some circumstances, microbes might facilitate exceptional preservation of certain soft tissues during post-mortem decay through authigenic mineralization via replacement with phosphates or pyrite [18,[21][22][23]. The retention of primary soft-tissues within vertebrate bone has been suggested to be enhanced by porosity and permeability reduction from mineral precipitation by microbial biofilms within the bone that are involved in the decomposition of organic matter at early taphonomic stages [23].…”

“…Briefly, all metagenomics reads were mapped back to each MAG with "strict" (exact match) and "permissive" (allowing 3 mismatches) options. The mapped reads from each MAG were then reassembled using SPAdes v3.13.0 [47] and a set of k-mer sizes (21,33,55,77) in MetaWRAP v0.8 [33]. The quality of the reassembled MAGs were assessed with CheckM v1.0.11 [46] and those MAGs with a minimum completeness of 90% and a maximum contamination of 10% were retained for downstream analyses.…”