Viruses Occur Incorporated in Biogenic High-Mg Calcite from Hypersaline Microbial Mats

Biofilms in modern CaCO3-supersaturated freshwater environments reveal viral proxies

Biofilms are mucilaginous-organic layers produced by microbial activity including viruses. Growing biofilms form microbial mats which enhance sediment stability by binding particles with extracellular polymeric substances and promoting growth through nutrient cycling and organic matter accumulation. They preferentially develop at the sediment-water interface of both marine and non-marine environments, and upon the growing surfaces of modern tufa and travertine. In this context, however, little is known about the factors, environmental or anthropogenic, which affect viral communities in freshwater spring settings. To explore this issue, geochemical and metagenomic data were subjected to multidimensional analyses (Principal Component Analysis, Classical Multidimensional Scaling, Partial Least Squares analysis and cluster analysis based on beta-diversity), and these show that viral composition is specific and dependent on environment. Indeed, waters precipitating tufa and travertine do vary in their geochemistry with their viruses showing distinct variability between sites. These differences between virus groups allow the formulation of a viral proxy, based on the Caudoviricetes/Megaviricetes ratio established on the most abundant groups of viruses. This ratio may be potentially used in analysing ancient DNA preserved in carbonate formations as an additional source of information on the microbiological community during sedimentation.

Mechanism of bacteriophage-induced vaterite formation

This study shows how bacterial viruses (bacteriophages, phages) interact with calcium carbonate during precipitation from aqueous solution. Using electron microscopy, epifluorescence microscopy, X-ray diffraction, and image analysis, we demonstrate that bacteriophages can strongly influence the formation of the vaterite phase. Importantly, bacteriophages may selectively bind both amorphous calcium carbonate (ACC) and vaterite, and indirectly affect the formation of structural defects in calcite crystallites. Consequently, the surface properties of calcium carbonate phases precipitating in the presence of viruses may exhibit different characteristics. These findings may have significant implications in determining the role of bacterial viruses in modern microbially-rich carbonate sedimentary environments, as well as in biomedical technologies. Finally, the phage-vaterite system, as a biocompatible material, may serve as a basis for the development of promising drug delivery carriers.

Viruses participate in the organomineralization of travertines

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.

SARS-CoV-2 removal with a polyurethane foam composite

The pandemic of COVID-19 (SARS-CoV-2 disease) has been causing unprecedented health and economic impacts, alerting the world to the importance of basic sanitation and existing social inequalities. The risk of the spread and appearance of new diseases highlights the need for the removal of these pathogens through efficient techniques and materials. This study aimed to develop a polyurethane (PU) biofoam filled with dregs waste (leftover from the pulp and paper industry) for removal SARS-CoV-2 from the water. The biofoam was prepared by the free expansion method with the incorporation of 5wt% of dregs as a filler. For the removal assays, the all materials and its isolated phases were incubated for 24 h with an inactivated SARS-CoV-2 viral suspension. Then, the RNA was extracted and the viral load was quantified using the quantitative reverse transcription (RT-qPCR) technique. The biofoam (polyurethane/dregs) reached a great removal percentage of 91.55%, whereas the isolated dregs waste was 99.03%, commercial activated carbon was 99.64%, commercial activated carbon/polyurethane was 99.30%, and neat PU foam reached was 99.96% for this same property and without statistical difference. Those new materials endowed with low cost and high removal efficiency of SARS-CoV-2 as alternatives to conventional adsorbents.

A Polyplex in a Shell: The Effect of Poly(aspartic acid)-Mediated Calcium Carbonate Mineralization on Polyplexes Properties and Transfection Efficiency

Mineralization by exposure of organic templates to supersaturated solutions is used by many living organisms to generate specialized materials to perform structural or protective functions. Similarly, it was suggested that improved robustness acquired through mineralization under natural conditions could be an important factor for virus survival outside of a host for better transfection of cells. Here, inspired by this fact, we developed a nonviral tricomponent polyplex system for gene delivery capable of undergoing mineralization. First, we fabricated anionic polyplexes carrying pDNA by self-assembly with a lipid-modified cationic polymer and coating by poly(aspartic acid). Then, we submitted the polyplexes to a two-step mineralization reaction to precipitate CaCO₃ under various supersaturations. We carried out detailed morphological studies of the mineralized polyplexes and identified which parameters of the fabrication process were influential on transfection efficiency. We found that mineralization with CaCO₃ is efficient in promoting transfection efficiency as long as a certain Ca²⁺/CO₃^2- lower limit ratio is respected. However, calcium incubation can also be used to achieve similar effects at higher concentrations depending on polyplex composition, probably due to the formation of physical cross-links by calcium binding to poly(aspartic acid). We proposed that the improved robustness and transfection efficiency provided by means of mineralization can be used to expand the possible applications of polyplexes in gene therapy.

Using Molecular Tools to Understand Microbial Carbonates

Here we review the application of molecular biological approaches to mineral precipitation in modern marine microbialites. The review focuses on the nearly two decades of nucleotide sequencing studies of the microbialites of Shark Bay, Australia; and The Bahamas. Molecular methods have successfully characterized the overall community composition of mats, pinpointed microbes involved in key metabolisms, and revealed patterns in the distributions of microbial groups and functional genes. Molecular tools have become widely accessible, and we can now aim to establish firmer links between microbes and mineralization. Two promising future directions include “zooming in” to assess the roles of specific organisms, microbial groups, and surfaces in carbonate biomineralization and “zooming out” to consider broader spans of space and time. A middle ground between the two can include model systems that contain representatives of important microbial groups, processes, and metabolisms in mats and simplify hypothesis testing. These directions will benefit from expanding reference datasets of marine microbes and enzymes and enrichments of representative microbes from mats. Such applications of molecular tools should improve our ability to interpret ancient and modern microbialites and increase the utility of these rocks as long-term recorders of microbial processes and environmental chemistry.

Fungi and viruses as important players in microbial mats

Microbial mats are compacted, surface-associated microbial ecosystems reminiscent of the first living communities on early Earth. While often considered predominantly prokaryotic, recent findings show that both fungi and viruses are ubiquitous in microbial mats, albeit their functional roles remain unknown. Fungal research has mostly focused on terrestrial and freshwater ecosystems where fungi are known as important recyclers of organic matter, whereas viruses are exceptionally abundant and important in aquatic ecosystems. Here, viruses have shown to affect organic matter cycling and the diversity of microbial communities by facilitating horizontal gene transfer and cell lysis. We hypothesise fungi and viruses to have similar roles in microbial mats. Based on the analysis of previous research in terrestrial and aquatic ecosystems, we outline novel hypotheses proposing strong impacts of fungi and viruses on element cycling, food web structure and function in microbial mats, and outline experimental approaches for studies needed to understand these interactions.

Between a Rock and a Soft Place: The Role of Viruses in Lithification of Modern Microbial Mats

Stromatolites are geobiological systems formed by complex microbial communities, and fossilized stromatolites provide a record of some of the oldest life on Earth. Microbial mats are precursors of extant stromatolites; however, the mechanisms of transition from mat to stromatolite are controversial and are still not well understood. To fully recognize the profound impact that these ecosystems have had on the evolution of the biosphere requires an understanding of modern lithification mechanisms and how they relate to the geological record. We propose here viral mechanisms in carbonate precipitation, leading to stromatolite formation, whereby viruses directly or indirectly impact microbial metabolisms that govern the transition from microbial mat to stromatolite. Finding a tangible link between host-virus interactions and changes in biogeochemical processes will provide tools to interpret mineral biosignatures through geologic time, including those on Earth and beyond.

Life and its traces in Antarctica's McMurdo Dry Valley paleolakes: a survey of preservation

The extremely cold and arid conditions of Antarctica make it uniquely positioned to investigate fundamental questions regarding the persistence of life in extreme environments. Within the McMurdo Dry Valleys and surrounding mountain ranges are multiple ancient relict lakes, paleolakes, with lacustrine deposits spanning from thousands to millions of years in age. Here we present data from light microscopy, scanning electron microscopy, electron dispersive x-ray spectroscopy, and radiocarbon dating to catalog the remarkable range of life preserved within these deposits. This includes intact microbes and nanobacteria-sized cocci, CaCO₃ precipitations consistent with biogenic calcium, previously undescribed net-like structures, possible dormant spores, and long-extinct yet exquisitely preserved non-vascular plants. These images provide an important reference for further microbiome investigations of Antarctic paleolake samples. In addition, these findings may provide a visual reference for the use of subsurface groundwater microbial communities as an analog for paleolake subsurface water on planets such as Mars.

The structure and role of the "petola" microbial mat in sea salt production of the Sečovlje (Slovenia)

Microbial mats are commonly observed in estuaries and in salt marshes but they only rarely represent a significant surface involved in salt production. In the Sečovlje salt works in Northern Adriatic, a microbial mat known as the "petola" covers the bottom of salt crystallising pans, highly influencing salt composition and salt production processes. Throughout the year the petola is subjected to numerous co-varying factors that drive changes in its structure and the microbial community. Seasonal modifications were investigated via various methods (cryo-HRSEM, XRD, elemental analysis, carbohydrate content, bacterial community structure). This study provides knowledge on microbial mat compositional characteristics and functional roles in response to seasonal variation in environmental conditions. The in situ characterisation (close-to its natural hydrated state) of the three-dimensional microstructure provides precise information about dominating filamentous cyanobacterium Coleofasciculus chthonoplastes and extracellular polymer secretion (EPS) organisation. This is the first study to address how microbial mat composition and structure, especially 3D EPS network (and microbial diversity), affects the salt production processes within a hypersaline environment.

Novel T4 bacteriophages associated with black band disease in corals

Research into causative agents underlying coral disease have focused primarily on bacteria, whereas potential roles of viruses have been largely unaddressed. Bacteriophages may contribute to diseases through the lysogenic introduction of virulence genes into bacteria, or prevent diseases through lysis of bacterial pathogens. To identify candidate phages that may influence the pathogenicity of black band disease (BBD), communities of bacteria (16S rRNA) and T4-bacteriophages (gp23) were simultaneously profiled with amplicon sequencing among BBD-lesions and healthy-coral-tissue of Montipora hispida, as well as seawater (study site: the central Great Barrier Reef). Bacterial community compositions were distinct among BBD-lesions, healthy coral tissue and seawater samples, as observed in previous studies. Surprisingly, however, viral beta diversities based on both operational taxonomic unit (OTU)-compositions and overall viral community compositions of assigned taxa did not differ statistically between the BBD-lesions and healthy coral tissue. Nonetheless, relative abundances of three bacteriophage OTUs, affiliated to Cyanophage PRSM6 and Prochlorococcus phages P-SSM2, were significantly higher in BBD-lesions than in healthy tissue. These OTUs associated with BBD samples suggest the presence of bacteriophages that infect members of the cyanobacteria-dominated BBD community, and thus have potential roles in BBD pathogenicity.

Biomineralization State of Viruses and Their Biological Potential

In nature, viruses can realize self-mineralization under metal-ion-abundant conditions. Interestingly, the mineralized state is a transition state of the virus when the host is not available. Mammalian viruses that share the similar chemical properties also stand a chance of transformation into a mineralized state. In this review, we focus on the possibility of mammalian viruses to undergo mineralization under a physiological environment and the development of biomineralized-based virus engineering. We will introduce the effect of biomineralization on the physiochemical or biological properties of viruses and we will discuss the relationship between mineral composition and biological potentials. The new biological prospects of mineralized-state viruses, including bypassing biological barriers, protection, and virus-host recognition, will provide new insight for the biosecurity and prevention of viral infection. With respect to vaccines, the mineralized state can modulate the immune recognition, change the immunization route, and elevate the vaccine efficacy. Together, these findings of the mineralized state of the virus may lead to a new understanding of virus biology, application, and prevention.