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

Abstract

Background: Exceptional preservation of endogenous organics such as collagens and blood vessels has been frequently reported in Mesozoic dinosaur fossils. The persistence of these soft tissues in Mesozoic fossil bones has been challenged because of the susceptibility of proteins to degradation and because bone porosity allows microorganisms to colonize the inner microenvironments through geological time. Although protein lability has been studied extensively, the genomic diversity of microbiomes in dinosaur fossil bones and their potential roles in bone taphonomy remain underexplored. Genome-resolved metagenomics was performed, therefore, on the microbiomes recovered from a Late Cretaceous Centrosaurus bone and its encompassing mudstone in order to provide insight into the genomic potential for microbial alteration of fossil bone. Results: Co-assembly and binning of metagenomic reads resulted in a total of 46 high-quality metagenomeassembled genomes (MAGs) affiliated to six bacterial phyla (Actinobacteria, Proteobacteria, Nitrospira, Acidobacteria, Gemmatimonadetes and Chloroflexi) and 1 archaeal phylum (Thaumarchaeota). The majority of the MAGs represented uncultivated, novel microbial lineages from class to species levels based on phylogenetics, phylogenomics and average amino acid identity. Several MAGs from the classes Nitriliruptoria, Deltaproteobacteria and Betaproteobacteria were highly enriched in the bone relative to the adjacent mudstone. Annotation of the MAGs revealed that the distinct putative metabolic functions of different taxonomic groups were linked to carbon, nitrogen, sulfur and iron metabolism. Metaproteomics revealed gene expression from many of the MAGs, but no endogenous collagen peptides were identified in the bone that could have been derived from the dinosaur. Estimated in situ replication rates among the bacterial MAGs suggested that most of the microbial populations in the bone might have been actively growing but at a slow rate.

Leave no stone unturned: individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core

“…In order to taxonomically resolve the eight recovered Thaumarchaeota genomes, we compared them to Ca. Nitrosocosmicus genomes that had been isolated or metagenomically assembled from diverse environments from around the world (Table S7 ) ranging from the arctic soil [ 62 ], tar-contaminated soil [ 63 ], vegetable field [ 64 ], dinosaur fossil [ 65 ] to wastewater filters [ 66 ]. High ANI (93.0–99.8%) (Fig.…”

Ultraviolet Autofluorescence Microscopy of Nanotyrannus lancensis Sections Reveals Blood Clots in Vessel Canals

“…We maintain that preservative fixed the bodies and internal organelles of living nematodes within the Nanotyrannus and Triceratops specimens, yielding the superior preservation and detail seen here. It should not be surprising to find nematodes, given the large numbers of microbes that have been found inhabiting dinosaur bones [46].…”

Perspectivas atuais sobre tecidos moles não mineralizados em fósseis de dinossauros não avianos

“…Por outro lado, apesar de um vasto conjunto de pesquisas relatarem tais achados, o ceticismo em relação à reivindicação de material orgânico original persiste e o assunto ainda hoje permanece controverso (Briggs et al, 1997, Buckley et al, 2008, Kaye et al, 2008, Pevzner et al, 2008, Bern, 2009, Buckley et al, 2017, Thomas & Taylor, 2019, Saitta et al, 2019, Liang et al, 2020. Mais especificamente em relação aos dinossauros não avianos, outra pesquisa avaliou amostras fósseis de oito indivíduos e relatou tecidos não mineralizados em seis espécies (Bertazzo et al, 2015).…”

“…Sabe-se, até o presente, que os tecidos moles não mineralizados representam desafios únicos ao fluxo de trabalho molecular, visto que tais componentes moleculares originais possuem baixo potencial de preservação. Portanto, aparentemente não poderiam persistir durante enormes intervalos de tempo (Eglinton & Logan, 1991, Schweitzer et al, 2009, Wadsworth & Buckley, 2014, Liang et al, 2020.…”

“…A mais antiga sequência de DNA original em quantidade significativa extraída de núcleos de gelo foi datada de cerca de 700 mil anos (Willerslev et al, 2007). Outro ponto de discussão recente se concentra em torno de relato de possível DNA de bactérias dentro de ossos fósseis de um representante de dinossauro não aviano do gênero Centrosaurus (Liang et al, 2020).…”