Viruses participate in the organomineralization of travertines

Abstract

Travertines, which precipitate from high temperature water saturated with calcium carbonate, are generally considered to be dominated by physico-chemical and microbial precipitates. Here, as an additional influence on organomineral formation, metagenomic data and microscopic analyses clearly demonstrate that highly diverse viral, bacterial and archaeal communities occur in the biofilms associated with several modern classic travertine sites in Europe and Asia, along with virus-like particles. Metagenomic analysis reveals that bacteriophages (bacterial viruses) containing icosahedral capsids and belonging to the Siphoviridae, Myoviridae and Podoviridae families are the most abundant of all viral strains, although the bacteriophage distribution does vary across the sampling sites. Icosahedral shapes of capsids are also the most frequently observed under the microscope, occurring as non-mineralized through to mineralized viruses and virus-like particles. Viruses are initially mineralized by Ca-Si amorphous precipitates with subordinate Mg and Al contents; these then alter to nanospheroids composed of Ca carbonate with minor silicate 80–300 nm in diameter. Understanding the roles of bacteriophages in modern carbonate-saturated settings and related organomineralization processes is critical for their broader inclusion in the geological record and ecosystem models.

Influence of different sample preparation techniques on imaging viruses and virus-like particles by scanning electron and scanning transmission electron microscopes

“…Biofilm samples may arouse controversy because it is commonly assumed that the biofilm contains mineralized or partially mineralized viruses and that they occur often in agglomerates ( Pradhan et al, 2022 ) or are included in the EPS ( Słowakiewicz et al, 2023 ). Distinguishing nanometer-sized viruses from other mineral particles still causes problems mainly because a compositional analysis may be distorted by a mineral growing on the virus.…”

“…Three biofilm samples covering the active depositional surface of carbonate travertines or interlayered with travertine were collected from Terme di Saturnia (42°39′31.23″N, 11°30′59.61″E; Italy), Pamukkale (37°55′24.46″N, 29°07′23.28″E), and Karahayıt “Kızılsu” (37°58′2.42″N, 29°6′9.30″E; Turkey) ( Słowakiewicz et al, 2023 ). In total, 0.1–0.8 g of each biofilm sample, depending on the expected concentration of viruses, was placed in a sterile Eppendorf tube; 2% glutaraldehyde was added to equalize the weight of each Eppendorf tube to 1 g. The samples were subsequently stored in the fridge at 4°C for 15 min.…”

Methanogen-mediated dolomite precipitation in an early Permian lake in northwestern China

“…δ 26 Mg, δ 13 C, and δ 18 O values in dolomite nodules. showing virus-like mineralized particles, some of which are hexagonal from the travertine at the Bešeňová site (Słowakiewicz et al, 2023). Note that the shapes of the nanoglobules is imperfect spheroids, but they appear as polyhedrons with flat surfaces and edges, resembling the icosahedral geometry of viral capsids (dashed line).…”

“…(C) Scanning electron microscope image showing viruses attached to a bacterium and viral-like particles within a cluster from a hypersaline microbial mat (Mesaieed sabkha, Qatar; Perri et al, 2018). (D) Transmission electron microscopy viewshowing virus-like mineralized particles, some of which are hexagonal from the travertine at the Bešeňová site(Słowakiewicz et al, 2023). Note that the shapes of the nanoglobules is imperfect spheroids, but they appear as polyhedrons with flat surfaces and edges, resembling the icosahedral geometry of viral capsids (dashed line).…”

Methanogen‐Mediated Precipitation of Mn Carbonates at the Expense of Mn Oxides

“…In marine environments, microbial sulfate reduction and methanogenic processes often induce the formation of carbonate minerals (H. L. Dong et al., 2022; Vasconcelos et al., 1995). In particular, microbially induced carbonate precipitation proceeded by creating supersaturated alkaline environments and through adsorption of cations by extracellular polymeric substances (EPS) generated by microbes, which acted as templates for mineral precipitation (H. L. Dong et al., 2022; Kenward et al., 2009; Lyu et al., 2020; Slowakiewicz et al., 2023). All these mechanisms were put forward from observations of modern sedimentary processes and laboratory simulation experiments, but deep‐time analogs are rarely reported so far, largely due to the lack of well‐preserved microbial fossils and EPS structures in ancient geological samples.…”