Iron-mediated mineralization and microbial overprints in soft tissue–like structures from a theropod dinosaur bone

The preservation of soft tissue–like structures in fossil vertebrate bones has been increasingly reported over the past two decades, yet their origin and preservation mechanisms remain debated. In this study, we investigated a fragment of theropod dinosaur bone using a multi-method microscopic and analytical approach to assess the nature, composition, and taphonomic context of structures morphologically resembling original soft tissues.

Optical microscopy and scanning electron microscopy (SEM) revealed abundant vessel-like structures characterized by tubular morphologies and fibrous wall architectures, as well as osteocyte-shaped lacunae with preserved canalicular networks. Energy-dispersive X-ray spectroscopy (EDS) demonstrated that many of these structures are permineralized predominantly by iron oxides, consistent with models proposing iron-mediated stabilization of organic substrates through early diagenetic mineral coatings. In addition, localized calcium fluoride mineralization was identified within some vascular casts, indicating chemically heterogeneous microenvironments and suggesting post-depositional fluid interactions. The occurrence of framboidal pyrite further points to transient anoxic conditions associated with organic-rich microdomains during early fossilization.

Histochemical staining revealed the presence of fungal hyphae and spores within some amorphous, gelatinous structures, indicating secondary microbial colonization of the bone. Two distinct fungal morphotypes were observed; however, not all translucent and elastic structures exhibited fungal staining. Importantly, confocal laser scanning microscopy combined with protein-specific fluorescent probes detected proteinaceous material selectively associated with vessel-like structures, while fungal elements showed distinct staining patterns. This spatially resolved signal supports the presence of endogenous protein remnants, likely representing degraded collagen or collagen-derived compounds, rather than purely microbial biofilms.

Together, these results demonstrate that fossil bone can preserve a complex assemblage of original biological residues, diagenetic mineral phases, and later microbial overprints. Iron-rich mineralization appears to play a critical role in the long-term stabilization of soft tissue–derived structures, while localized geochemical conditions govern the diversity of preservation pathways. Our findings contribute to a growing framework of molecular taphonomy and highlight the importance of integrated morphological, chemical, and biochemical analyses in evaluating claims of soft tissue preservation in deep time.