TWiM #291: Biogeography of Tectonics and Teeth

1. Paper Abstracts

1.1. Snippet paper; discussion starts at 05:23 minutes

“Plate tectonics distinguishes Earth from the other terrestrial planets but its initiation mechanism and onset time are debated. We propose plate tectonics was initiated by the deposition of magnetite-rich banded iron formations (BIFs) through biogeochemical iron cycling in Neoarchean oceans. In the photic zone of proto-continental margins, photoferrotrophic bacteria efficiently oxidized the dissolved Fe(II) and induced massive precipitation of ferric oxyhydroxide, which would rapidly react with Fe(II)-rich hydrothermal fluids from coeval vigorous volcanism in Neoarchean oceans to produce magnetite-rich BIFs. Mechanical models demonstrate that the localization of high-density BIF deposition near proto-continents induces collapse of the lithosphere and can initiate the earliest subduction. The peak deposition of BIFs in 2.75–2.40 Ga provides a time constraint on the inception of plate tectonics.” (Zhang et al. 2023, no changes)

1.2. Main paper; discussion starts at 29:01 minutes

“Streptococcus mutans has been implicated as the primary pathogen in childhood caries (tooth decay). While the role of polymicrobial communities is appreciated, it remains unclear whether other microorganisms are active contributors or interact with pathogens. Here, we integrate multi-omics of supragingival biofilm (dental plaque) from 416 preschool-age children (208 males and 208 females) in a discovery-validation pipeline to identify disease-relevant inter-species interactions. Sixteen taxa associate with childhood caries in metagenomics-metatranscriptomics analyses. Using multiscale/computational imaging and virulence assays, we examine biofilm formation dynamics, spatial arrangement, and metabolic activity of Selenomonas sputigena, Prevotella salivae and Leptotrichia wadei, either individually or with S. mutans. We show that S. sputigena, a flagellated anaerobe with previously unknown role in supragingival biofilm, becomes trapped in streptococcal exoglucans, loses motility but actively proliferates to build a honeycomb-like multicellular-superstructure encapsulating S. mutans, enhancing acidogenesis. Rodent model experiments reveal an unrecognized ability of S. sputigena to colonize supragingival tooth surfaces. While incapable of causing caries on its own, when co-infected with S. mutans, S. sputigena causes extensive tooth enamel lesions and exacerbates disease severity in vivo. In summary, we discover a pathobiont cooperating with a known pathogen to build a unique spatial structure and heighten biofilm virulence in a prevalent human disease.” (Cho et al. 2023, no changes)

2. Vision and Change Core Concepts and 2024 ASM Fundamental Statements

3.  Potential Learning Objectives for the Podcast

¹ Papers: Snippet (S) or Main (M)

²Learning Objectives: Lower Order or Higher Order (H)

4. Techniques Described (with Time Stamps)

Here is a link to a bio-dictionary that has many, but not all terms if you need a definition: Explore Biology Bio-Dictionary

4.1. Snippet Paper

• Geological Evidence (11:10–21:30): This is evidence taken from the earth, including fossils and sediment layer.  Here, analysis of geological evidence, particularly banded iron formations, or large and dense deposits of iron oxides, allowed the researchers to see where photoferrotroph activity was present and how it may have influenced plate tectonics.
• Geodynamic Modeling (24:56–26:40): Computational models of geologic events were used to evaluate the role of photoferrotrophic bacteria in initiating plate tectonics on early Earth.

4.2. Main Paper

• In vivo Virulence Assay (45:49–47:03; 49:21–50:18): These are assays for virulence conducted in animals.  Here, the rodent models allowed researchers to study microbial interactions and disease development, including colonization and disease severity, in a living system.
• In vitro Virulence Assay (49:21–52:40): These are assays for virulence conducted in plates or tubes.  Here, biofilm development and biogeography was investigated in vitro, or in a test tube environment, and the results were shown to be consistent with those in the rodent models.
• Mander’s Overlap Coefficient (50:18–52:07): This is a technique/method to quantify the degree of spatial proximity of two different fluorescence signals in relation to each other. In the paper, it was used to evaluate the spatial proximity between a newly identified species (associated with caries) to either S. mutans, or the extracellular polysaccharides produced by S. mutans.

5. Connections to General Microbiology Processes/Concepts (with Time Stamps)

5.1. Snippet Paper

• Oxidation-reduction Reactions (5:23–7:40; 11:10–13:59; 15:43–18:49): The conversion of ferrous iron (Fe2+) into ferric iron (Fe3+) takes place naturally in the ocean when oxygen oxidizes ferrous iron dissolved in the water, causing ferric iron to precipitate. Anaerobic photoferrotrophs, such as the ones discussed here, are able to oxidize ferrous iron themselves, providing them with a source of electrons.
• Toxicity of Oxygen (8:57–9:00): The early Earth was a low oxygen environment, and photosynthesizing cyanobacteria transformed the planet’s atmosphere by letting out large quantities of oxygen gas. This ushered in a mass extinction event, as many organisms were unable to cope with this change in environment and died out. The early oceans were anoxic, as they took place before this oxygenation event, providing an environment where organisms could oxidize ferrous iron for an electron source.
• Chemotrophy vs Phototrophy (11:10–13:59; 15:43–18:49): Chemotrophs use the oxidation of electron donors as a source of energy, whereas phototrophs use light for energy. Photoferrotrophs live in photic zones of the ocean and obtain light energy from the sun.
• Anoxygenic vs Oxygenic Phototrophy (11:10–13:59; 15:43–18:49): Oxygenic phototrophs split water to obtain electrons and release oxygen as a byproduct of their photosynthesis. Anoxygenic phototrophs, such as the photoferrotrophs of this article, lived in the anoxic ocean and used ferrous iron as electron donors.
• Diversity of Carbon Fixation Pathways (11:10–15:21; 20:30–21:30): Rather than using rubisco, like plants do, for example, many bacteria bring carbon dioxide into the carbon-fixation calvin cycle through running the TCA cycle in reverse. This includes many green sulfur bacteria and purple non-sulfur bacteria that oxidize ferrous iron.

5.2. Main Paper

• Mechanisms of Pathogenesis (29:01–52:12): The dividing S. sputigena that have become trapped form large multicellular “honeycomb” structures that trap S. mutans. The trapped S. mutans break down fermentable carbon sources and release lactic acid. This lactic acid, which is concentrated due to the S. mutans being immobilized in these honeycomb structures, lowers the pH beyond what the enamel of the teeth can tolerate, leading to the breakdown of enamel and formation of dental caries.
• Symbiosis (29:01–30:07; 37:55–38:36; 40:45–48:20; 50:18–52:12): Selenomonas sputigena is a pathobiont that cooperates with Streptococcus mutans. S. sputigena forms a honeycomb-like multicellular superstructure around S. mutans, allowing the acid produced by S. mutans to build up on the surface of a tooth. This cooperation benefits S. sputigena by allowing it to invade beyond the gumline into a new niche. This interaction also increases the virulence of S. mutans. While this symbiotic relationship benefits the microbes, the host is harmed due to increased development of caries.
• Opportunistic Infections (29:01–30:07, 32:46–37:45; 40:45–44:58, 45:49–47:03; 47:33–48:11; 52:40  -54:14): S. sputigena is normally found in the upper respiratory tract, and it is unable to cause damage to enamel by itself. S. sputigena can enhance the damage caused by S. mutans to levels beyond what the bacteria would normally cause by trapping S. mutans and concentrating its acidic metabolic products in one area. This lowers the local pH and leads to enhanced enamel decay.
• Human Microbiome (32:46–37:45; 37:55–38:36; 38:58–40:06; 40:45–44:58): The human microbiome is a delicate balance that can become disturbed and fall into a state that brings harm to the human host when new microbes, or in this case, a new combination of microbes, makes a host its home. This article highlights how S. sputigena and S. mutans co-infecting the human mouth can lead to the development of caries by contributing to acidic biofilms on tooth surfaces. An important aspect of this is that these organisms can become trapped in biofilms that not only allow them to cause damage to an individual’s first set of teeth, but also their permanent teeth over a long period of time.
• Biofilm (32:46–37:45; 38:58–39:26; 40:45–44:58; 50:18–52:07): Biofilms are matrix structures that bacteria form that confer advantages such as protection from extracellular environments and host defenses or facilitating bacteria communication and nutrient exchange. S. mutans secretes polysaccharides that form a biofilm, trapping S. sputigena.
• Fermentation (32:46–37:45): Bacteria contained in these oral biofilms, such as S. mutans, can ferment carbohydrates to produce organic acids, especially lactic acid. The accumulation of this product leads to lowered pH levels, eroding the enamel of the teeth.
• Flagella (40:45–44:58): The flagella, a long tube structure made of flagellin proteins, confers motility to microorganisms. S. sputigena is a flagellated organism, but this motility is lost when the bacteria becomes trapped in oral biofilms. This leads to S. sputigena dividing in one place and forming the large honeycomb structures which trap S. mutans.
• Control of Microbes (40:06–end time): Bacteria in biofilms can promote caries formation in the oral cavity. Despite the connection between caries formation and bacteria, caries are not treated with antimicrobials because the bacterial species diversity is too great in the mouth. The impermeability of biofilms in the oral cavity also contributes to the ineffectiveness of using antibiotics to treat caries.
• Genomics and Transcriptomics (40:45–44:48; 49:21–50:18): Genomics, or the analysis of the genomes of organisms and transcriptomics, the analysis of what genes are being expressed by these organisms, were used in a study discussed to look for the presence of pathogens associated with caries. In addition to genomics allowing the researchers to identify 16 different taxa associated with caries in the population studied, transcriptomics allowed the researchers to see what genes were being expressed and hypothesize what processes were likely important to the progression of disease.

6. Podcast Questions

1. Which of the statements below most accurately describes the metabolic capabilities of photoferrotrophs?
   1. They capture light energy, oxidize ferrous iron (Fe2+) to ferric iron (Fe3+), and can fix CO2 into organic carbon.
   2. They capture light energy to oxidize hydrogen disulfide to sulfate, and can fix carbon dioxide into organic carbon.
   3. They require oxygen, hydrogen, and ATP to convert iron from ferric iron (Fe3+) to ferrous iron (Fe2+).
   4. They capture light energy to fix carbon dixoide into organic carbon, and produce oxygen as a by-product. NADH.
2. Photoferrotrophs are examples of one of the oldest phototrophic metabolisms on Earth. Which environmental conditions on early Earth were especially advantageous for photoferrotrophs?
   1. High temperatures in most ocean waters and also the presence of dissolved sulfides.
   2. Dark and continuous clouds that blocked the sunlight from reaching the Earth’s surface.
   3. Lower oxygen concentration in the ocean and more soluble ferrous iron (Fe2+).
   4. Presence of very little organic matter and high levels of  insoluble ferric iron (Fe3+).
3. Which of the following are evidence of the metabolic activity of photoferrotrophs in the ancient oceans?
   1. Seismographic detection of earthquake activity along the oceanic continental trenches.
   2. Magnetite-rich banded iron formations in 2.75- 2.4 billion year old rocks at continental margins.
   3. Geological formations resembling former hydrothermal vents near the continental slopes.
   4. Fossils resembling extant ocean fauna found at hydrothermal vents and in ocean gyres.
4. What activity of photoferrotrophs do authors, Zhang et al. 2023, suggest might have initiated plate tectonics?
   1. The metabolic consumption of iron oxides layers by photoferrotrophs weakening the lithosphere causing it to fracture and sink into the mantle.
   2. Photoferrotroph growth caused fractures in the crust that led to the formation of hydrothermal vents and the hydrothermal activity fractured the lithosphere.
   3. The metabolic activity of photoferrotrophs resulted in iron deposits, the weight of the iron deposits caused the lithosphere to fracture and sink into the mantle.
   4. The sheer number and weight of photoferrotrophic organisms growing on the ocean floor generated enough mass and force to sink the tectonic plates.
5. Based on the podcaster’s discussion of modern and ancient oceans, what oceanic change listed below would likely increase the abundance of photoferrotrophs?
   1. Decreasing the iron, which is toxic to photoferrotrophs.
   2. Decreasing the oxygen levels, which increases soluble iron.
   3. Increase the sunlight penetration, which is needed for ATP.
   4. Increase the water temperature, which activates enzymes.
6. Which of the following correctly describes the interaction between Selenomonas sputigena and Streptococcus mutans that leads to increased caries formation?
   1. S. sputigena releases cofactors that increase the activity of enzymes involved in lactic acid production of S. mutans.
   2. By-products of S. sputigena metabolism “activate” S. mutans, giving it the new ability to degrade enamel and cause cavities.
   3. S. mutans give S. sputigena acid producing capabilities through horizontal gene transfer, increasing cavity formation.
   4. Biofilms created by S. mutans immobilize S. sputigena, which trap S. mutans and concentrate lactic acid production on enamel.
7. Which of the following is an example of an in vivo experimental model?
   1. Biofilms were grown on a saliva-coated hydroxyapatite discs and the biomass density and growth quantified .
   2. Biofilms were formed on sterilized enamel specimens prepared from de-identified extracted human teeth.
   3. Bacterial colonization on teeth and their impact on disease onset were assessed with a rodent caries model.
   4. Acid tolerance tests were performed using Brain Heart Infusion broth to assess the growth of single bacterial species.

7. Figure Reading Exercises

The following are two figure reading exercises, both from the main paper (Figures 5 and 9).

7.1. First Figure Reading Exercise

7.2.2. Questions

1. In panel A, what does the red channel in the column labeled “SM + SS” represent?
   1. The spatial structure of S. sputigena in a mixed biofilm.
   2. The spatial structure of S. mutans in a mixed biofilm.
   3. The spatial structure of polysaccharides in a mixed biofilm.
   4. The spatial structure of P. salivae in a mixed biofilm.
2. What does the bar height in panel C indicate?
   1. median of biofilm volume
   2. mean of biofilm volume
   3. standard deviation of biofilm volume
   4. standard error of biofilm volume
3. Which dual growth condition produced the smallest S. mutants biofilm (panel C)?
   1. growth with S. sputigena
   2. growth with L. wadei
   3. growth with P. salivae
   4. growth of two S. mutans
4. How is the growth of S. sputigena impacted by the inclusion of S. mutans in the biofilm (panel C)?
   1. S. sputigena had decreased growth when S. mutans was included in the biofilm and this is statistically significant
   2. S. sputigena growth was not different when S. mutans was included because the difference was not statistically significant.
   3. S. sputigena had increased growth when S. mutans was included in the biofilm and this is statistically significant
   4. S. sputigena had increased growth when S. mutans was included , but the difference was not statistically significant.
5. Which species showed association primarily with the extracellular polysaccharide matrix rather than to S. mutans cells (panel E)? [pick all that apply]
   1. S. sputigena
   2. P. salivae
   3. L. wadei
   4. None 

7.2. Second Figure Reading Exercise

7.2.2. Questions

1. Rodents were fed a sugar-rich diet (panel A; cariogenic diet) during the experiments. What is the primary reason for this?
   1. The researchers wanted to test the impact of different levels of sugars on tooth lesion formation.
   2. Exposure to high-sugar diets results in drastic changes in body weight and overall health.
   3. Exposure to high-sugar diets is a common characteristic contributor of early childhood caries.
   4. Exposure to direct-use carbon sources for the bacteria would have the most likely success.
2. Quantitative polymerase chain reaction (qPCR) was used to assay infection by all the species used in the infection protocol even if the bacterium was not in the culture (panel A and C).  Why was this an important control?
   1. This confirms that the bacteria infecting the animal is that species.  It ensures there was no accidental cross-contamination.
   2. This confirms that the bacteria infecting the animal is not harmful. It ensures the infection was safely administered.
   3. This confirms that the bacteria infecting the animal is well studied. It ensures the results will be easy to interpret.
   4. This confirms that the bacteria infecting the animal is genetically stable. It ensures the strain will not mutate rapidly.
3. What does a dark blue box in the qPCR results indicate (panel C)? [pick all that apply]
   1. high bacterial infection
   2. high body weight
   3. high bacterial DNA detection
   4. high tooth decay and lesions
4. What do the results shown in the qPCR graphs (panel C) indicate for this whole experiment (panels C-F)? [pick all that apply]
   1. This would indicate that SM and SS were not able to grow on rat model tooth surfaces.
   2. SM and SS bacteria were both able to grow on the rodent model tooth surfaces.
   3. The specific species used in the infection were the only ones present in the rodents.
   4. Effects on weight and tooth lesions cannot  be attributed to specific bacterial infections.
   5. Effects on weight and tooth lesions can be attributed to specific bacterial infections.
5. Body weight was tracked to identify whether the treatments affected the rodent health (panel C).  What does the bar height indicate?  Did the treatment affect the rodent’s health?
   1. median of weight; no, the differences were not significant.
   2. mean of weight ; no, the differences were not significant.
   3. standard deviation of weight; yes, the differences were significant
   4. standard error of weight; yes, the differences were significant
6. Keyes scores is a measure of lesions.  Both lesions (panel E) and severe lesions (panel F) are quantified for all rodent treatments. What do these results indicate about the abilities of the bacteria to cause tooth decay? [pick all that apply]
   1. S. sputigena is not able to effectively cause enamel lesions on its own.
   2. S. mutans is not able to effectively cause enamel lesions on its own.
   3. S. sputigena is able to effectively cause enamel lesions on its own.
   4. S. mutans is able to effectively cause enamel lesions on its own.
   5. Co-infection causes more enamel lesions than S. mutans alone.
   6. Co-infection causes more enamel lesions than S. sputigena alone.
   7. Co-infection reduces the number enamel lesions below the control.

8. Paper Information and Licensing

8.1. Snippet paper

• Zhang S, Li Y, Leng W, Gurnis M. 2023. Photoferrotrophic bacteria initiated plate tectonics in the Neoarchean. Geophys Res Lett. 50 (13). doi: 10.1029/2023GL103553.
• This is an open access article distributed under the terms of the Creative Commons CC BY 4.0 license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

8.2. Main paper

• Cho H, Ren Z, Divaris K, Roach J, Lin BM, Liu C, Azcarate-Peril MA, Simancas-Pallares MA, Shrestha P, Orlenko A, Ginnis J, North KE, Zandona AGF, Ribeiro AA, Wu D, Koo H. 2023. Selenomonas sputigena acts as a pathobiont mediating spatial structure and biofilm virulence in early childhood caries. Nat Commun. 14:2919-2938. doi: 10.1038/s41467-023-38346-3.
• This article is licensed under a Creative Commons Attribution (CC BY 4.0) International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. See the article’s copyright information.