Microbial Ecology

TWiM #236: Gossamer Wings and Symbionts on the Sea Bottom

Podcast and Annotation Information
  • Annotation by Karen Massihi, Ben Guerrero, and Matteo Veglia, Rebecca Seipelt-Thiemann, and Joanna Klein
  • Podcast audio by TWiM: Listen to TWiM #236 Podcast
  • Podcast transcript by Otter.ai and edited by Rebecca Seipelt-Theimann and Harshita Sharma: Access Podcast Transcripts
  • Papers Discussed:
    • Clement L, Dorman JB, McGee R. 2020. The Academic Career Readiness Assessment: Clarifying Hiring and Training Expectations for Future Biomedical Life Sciences Faculty. CBE Life Sci Educ. 19(2):ar22. doi: 10.1187/cbe.19-11-0235.
    • Hinzke T, Kleiner M, Meister M, Schlüter R, Hentschker C, Pané-Farré J, Hildebrandt P, Felbeck H, Sievert SM, Bonn F, Völker U, Becher D, Schweder T, Markert S. 2021. Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis. Elife. 10:e58371. doi: 10.7554/eLife.58371.

NOTE: The Snippet paper was not a scientific article, but was about mentoring graduate students, so it was not included in this annotation.

1. Paper Abstracts

1.1. Snippet paper; discussion starts at [n/a] minutes

  • n/a

1.2. Main paper; discussion starts at 20:00 minutes

The Most Interesting Things (according to students)

  • The discovery of bacterial differentiation within the tubeworm symbionts was incredible. Initially, it was thought that the different sizes and shapes of Endoriftia were different species. The bacteria found within the worms are all the same species but fulfill different roles and are different shapes.
  • The concept of chemosynthesis replacing photosynthesis in deep-sea environments was mind-blowing. These bacteria sustain an entire ecosystem without sunlight, using hydrogen sulfide as an energy source.

Abstract

“The deep-sea tubeworm Riftia pachyptila thrives in hydrothermal vent ecosystems through a symbiotic relationship with sulfur-oxidizing bacteria housed in its trophosome. Despite the symbiont population consisting of a single 16S rRNA phylotype, there is remarkable physiological heterogeneity, the various sizes the bacteria come in that are seen through electron microscope, among the bacteria. This study reveals a division of labor between smaller and larger symbiont cells. Smaller symbionts are primarily involved in the uptake and assimilation of inorganic nutrients, while larger symbionts focus on the synthesis and transfer of organic compounds to the host. This differentiation enhances the overall productivity and efficiency of the symbiotic partnership, providing insights into the complexity of host-microbe interactions in extreme environments.” (Hinzke et al. 2021, no changes).

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

 Snippet Main

Vision and Change Topics

 N/A
  • Microbial Ecology (V&C_ME)
  • Impact of Microorganisms (V&C_IM)

ASM Fundamental Statements

 N/A
  • Fundamental Statement 20 (ASM_20): Microbes are ubiquitous, found in diverse and dynamic ecosystems, where they use available resources and often form complex communities.
  • Fundamental Statement 25 (ASM_25): Microbes are used as models that provide fundamental knowledge about life processes.

3.  Potential Learning Objectives for the Podcast

The student will be able to: Paper1 Order2
  • Not applicable.

S

L
  • Not applicable.

S

H
  • Define symbiosis.
  • Identify the function of the morphologically different bacterial symbionts in the tubeworm.
  • Recall how bacteria utilize specific mechanisms to survive in harsh environments without sunlight and without conventional nutrients.

M

L
  • Predict the effect of changes to the symbiont relationship.

M

H

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 definitions if you need a definition: Explore Biology Bio-Dictionary

4.1. Snippet Paper

  • Not applicable.

4.2. Main Paper

  • Sampling (20:54–22:30; 37:24–38-58): Sampling from the environment is a key part of the effort to understand how and what microbes do as well as where. The podcasters discuss where the tubeworms exist, that is near hydrothermal vents in the ocean.
  • Bacterial Cell Identification (23:35–31:54): Many methods can be used to identify bacterial cells and this typically starts with microcopy to identify cell shape and size. The authors also used 16S rDNA as well as metabolomics to identify the cells.

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

5.1. Snippet Paper

  • n/a

5.2. Main Paper

  • Symbiosis (20:45–39:32): Symbiosis is close and long-term biological interaction between two different species. The podcast discusses the symbiotic relationship between Riftia pachyptila (giant tubeworms) and their bacterial symbionts. These bacteria live inside specialized cells (bacteriocytes) and provide the tubeworms with nutrients through chemosynthesis, making the relationship essential for survival in deep-sea hydrothermal vents.
  • Chemosynthesis (23:35–27:33): Chemosynthesis is the process by which certain organisms use chemical energy, rather than light energy, to produce organic compounds.Unlike photosynthetic organisms that use sunlight, the bacteria inside Riftia pachyptila use hydrogen sulfide (H₂S) as an energy source to fix carbon dioxide (CO₂) into organic molecules. This process sustains the tubeworms in the absence of sunlight at the ocean floor.
  • Cell size, Protein Composition, Gene Expression Profile (28:30–30:07): The different functions and various shapes of the Endoriftia bacterium result in different interactions in the host. Larger Endoriftia are digested by the worm and smaller ones are metabolically active. In this context, “size” typically refers to the physical dimensions of the tubeworm’s symbiotic structures (e.g., the trophosome), or the size of the bacterial cells colonizing the host. The researchers mentioned the size of the symbionts and the trophosome to illustrate how extensive colonization becomes during development. Microscopy helps determine how these bacterial populations expand and organize within the host tissue.

6. Podcast Questions

  1. Symbiosis is _______ .
    1. a close interaction between two or more species in a location.
    2. interactions among a community of all the same species.
    3. an overlap of local habitats where multiple species are present.
    4. chemical communication strategies used by the same species.
  2. What is the primary function of larger Endoriftia bacteria within the trophosome of Riftia pachyptila?
    1. They are responsible for photosynthetic metabolism.
    2. They are digested by the tubeworm to provide nutrients.
    3. They help the worm move through sludge and sediment.
    4. They control the tubeworm’s gene and protein expression.
  3. Which of the following best describes the role of smaller symbiont cells in the Riftia pachyptila symbiosis?
    1. Transfer of organic compounds to regions of need
    2. Transfer of metal cofactors necessary for metabolism
    3. Uptake and assimilation of inorganic compounds
    4. Lipid bilayer accumulation and mitochondrial division
  4. How do Endoriftia bacteria inside Riftia pachyptila obtain the energy needed to fix carbon and support the host?
    1. By oxidizing hydrogen sulfide to drive chemosynthesis
    2. By utilizing photons from sunlight via photosynthesis
    3. By filtering and then absorbing nutrients from seawater
    4. By digesting cells that the tubeworm sheds during molting
  5. What would you expect to find if the smaller Endoriftia cells were now unable to develop into the larger Endoriftia cells?
    1. The tubeworm would be found nearer the thermal vents.
    2. The tubeworm would not reach the height of 2 meters tall.
    3. The tubeworm would be unable to molt its chitin outer layer.
    4. The tubeworm would be unable to acquire as much nutrition.

7. Figure Reading Exercises

The following are two figure reading exercises, both from the main paper (Figures 3; Figure 6).

7.1. First Figure Reading Exercise

7.1.1. Learning Objectives

Students will be able to:

  • Identify key aspects of a heatmap.
  • Interpret a heatmap to identify abundance and other relevant features.
  • Correlate protein abundance patterns within Endoriftia subpopulations to cell functionally.
  • Predict how shifts in protein abundance might influence symbiont function and host-symbiont nutrient exchange.
Experimental Background (Hinzke et al., Figure 3)

Riftia pachyptila are tubeworms found at the ocean floor and can grow up to 2 meters tall. In exploring how these organisms are able to survive extreme pressure and lack of sunlight, Hinzke et al. (2021) identified that the tubeworm has a bacterial symbiont that despite having very different morphologies is the same bacterial species, Endoriftia. To gain a better understanding of how the different cell morphologies function, the researchers first sorted the bacterial cells by size and then performed techniques to identify and quantify the proteins that each cell morphology produces. Their results are displayed as a heatmap.

Heat map of gene expression by cell type and gene function group.
Figure 3. “Abundance trends of selected Endoriftia proteins of various functions in the four fractions XS to L. Trends are indicated by color shades from light green (lowest protein abundance across all four fractions) to dark green (highest abundance across all four fractions; note that colors do not allow comparison of protein abundance between proteins). Abundance values in the heat map are based on statistical evaluation of four biological replicates with sulfur-rich trophosomes (for abundance trends of sulfur-depleted samples refer to Figure 3—figure supplement 1 and Appendix section B). Proteins marked with asterisks show statistically significant trends, that is, differences that are consistent across all replicates in S-rich (left asterisk) or S-depleted specimens (right asterisk), or both (two asterisks). White cells indicate that this protein was not detected in this sample or too low abundant to be included in statistical analyses. For an overview of all identified symbiont proteins and their relative abundances and for a summary of protein abundance trends sorted by metabolic category see Supplementary files 2 and 3, respectively. Accession numbers refer to NCBI/JGI entries. SU: subunit, DUF: domain of unknown function, ss: single-stranded, transcr: transcription, assoc: associated, dep: dependent, HP: hypothetical protein, put: putative, oligopep: oligopeptide, ppc: periplasmic component, DHG: dehydrogenase: RubisCO: ribulose-1.5-bisphosphate carboxylase/oxygenase, Ox: oxidase, OxRed: oxidoreductase, PEP: phosphoenolpyruvate, fcc: flavocytochrome c, rhd: rhodanese, resp: respiratory, cat: catalytic, Vit: vitamin and cofactor metabolism.” (Hinzke et al. 2021, no changes)

7.1.2. Questions

  1. What does the intensity of the green color for each square represent?
    1. Abundance of a particular protein in the sample relative to the other samples
    2. Absence or a level too low to detect for a particular protein in the sample
    3. Abundance of a particular RNA in the sample relative to the other samples
    4. The frequency of finding a fully intact protein sample using mass spectroscopy
  2. What cell morphologies were assayed in this experiment? [pick all that apply]
    1. Extra small (XS)
    2. Small (S)
    3. Medium (M)
    4. Large (L)
    5. Extra large (XL)
  3. What cellular process is the protein FtsZ involved in?
    1. DNA topology
    2. Chemotrophy
    3. Cell cycle
    4. Transport
  4. The protein ClpB is most abundant in what size cell?
    1. XS
    2. S
    3. M
    4. L
    5. XL
  5. Some of the protein functional groups show exclusive or near exclusive abundance in cells of a particular size. What functional groups are consistently of high abundance in large cells, and what might this mean for function/role of the large cells?
    1. Chemotrophy, Nitrogen metabolism; all cells likely perform these functions since these proteins are found in all cell sizes.
    2. Chaperones and stress proteins, DNA topology; small cells likely perform these functions while large cells do not.
    3. DNA replication and repair, Vitamin and cofactor metabolism; large cells likely perform these functions while small cells do not.
    4. Carbon metabolism, Transport; all cells likely perform these functions since these proteins are found in all cell sizes.
  6. Some of the protein functional groups show exclusive or near exclusive abundance in cells of a particular size. What functional groups are consistently of high abundance in small/extra small cells, and what might this mean for function/role of these cells?
    1. Chemotrophy; all cells likely perform these functions since these proteins are found in all cell sizes.
    2. Chaperones and stress proteins; small cells likely perform these functions while large cells do not.
    3. DNA replication and repair, large cells likely perform these functions while small cells do not.
    4. Carbon metabolism; all cells likely perform these functions since these proteins are found in all sizes.
  7. FtsZ protein abundance is noted by the top row of cell cycle grouped functions. This protein is known to function in bacterial cell division. It is required to form the Z ring at the site of cell division. What would you predict if the large cells began to produce this protein?
    1. Large cells would die from the change in protein expression.
    2. Small cells would increase in size and bulge the tubeworm diameter.
    3. Large cells would likely not be found and more small cells would.
    4. Small cells would likely not be found, but become large cells.

7.2. Second Figure Reading Exercise

7.2.1. Learning Objectives

Students will be able to:

  • Identify key components in a model figure.
  • Evaluate the model figure to make conclusions about which cells would be located where based structural and biological features.
  • Evaluate the model figure to make conclusions about which cells would be involved in specific biological processes based on their structural features and locations.
Experimental Background (Hinzke et al., Figure 6)

Riftia pachyptila are tubeworms found at the ocean floor and can grow up to 2 meters tall. In exploring how these organisms are able to survive extreme pressure and lack of sunlight, Hinzke et al. (2021) identified that the tubeworm has a bacterial symbiont that despite having very different morphologies is the same bacterial species, Endoriftia. Using all of the results, they constructed a model of the symbiotic relationship which is shown in the schematic.

Schematic model for tubeworm:bacterial symbiosis.

Figure 6. “Schematic drawing of Riftia symbiont cells inside the trophosome. (A) An adult tubeworm reaches 2 m in body length. Its symbiont-containing organ, the trophosome (green), fills most of the body cavity (coelomic cavity), and is immersed in coelomic (non-vascular) blood (not shown). (B) Close-up of the lobular trophosome tissue. (C) Single lobule (200–500 µm in diameter) with interior blood vessels (blood-filled spaces) and symbiont cells visible. (D) Cross-section through a trophosome lobule (similar to that in Figure 5A) with small symbiont cells located in the center around an efferent blood vessel. Symbiont cell size increases toward the lobule periphery, where the largest symbionts are digested by the host (curls). Blood flow from lobule periphery to lobule center may cause gradients in nutrient availability. Based on the results of this study, the most striking characteristics of small and large symbionts, which determine their respective roles in the symbiosis, are indicated. Note that this is a simplified illustration, in which the various kinds of host cells (including their membranes, nuclei and organelles), as well as blood vessels or gonads that line the surface of the trophosome were omitted for clarity’s sake. (Illustrations based on drawings, TEM images and descriptions by van der Land and Nørrevang, 1977; Felbeck and Turner, 1995; Bright and Sorgo, 2003).” (Hinzke et al. 2021, no changes)

7.2.2. Questions

  1. Which of the following structures is a key component of the Riftia trophosome, and what color are these in the schematic drawing?
    1. Mantle; peach
    2. Lobule; green
    3. Gills; dark red
    4. Siphon; bright red
  2. In the Riftia trophosome, where are the largest symbiont cells typically located relative to blood flow?
    1. Evenly distributed throughout the lobule, near the outgoing blood
    2. Concentrated in the lobule center, away from the blood flow
    3. Predominantly in the lobule periphery, near the incoming blood
    4. The large cells circulate with the blood in the blood vessels
  3. Based on the schematic, which trophosome cells would be involved in chemosynthesis involving sulfur?
    1. Large Riftia cells
    2. Large Endorifitia cells
    3. Small Riftia cells
    4. Small Endoriftia cells
  4. Based on the schematic, which trophosome cells would have the greatest access to Riftia-generated nutrients?
    1. Large Endorifitia cells
    2. Medium Endorifitia cells
    3. Small Endoriftia cells
    4. Extra small Endorifitia cells
  5. Based on the schematic, which trophosome cells would likely have a greater localized concentration of carbon?
    1. Large Endorifitia cells
    2. Medium Endorifitia cells
    3. Small Endoriftia cells
    4. All the Endoriftia cells

8. Paper Information and Licensing

8.1. Snippet paper

  • Clement L, Dorman JB, McGee R. 2020. The Academic Career Readiness Assessment: Clarifying Hiring and Training Expectations for Future Biomedical Life Sciences Faculty. CBE Life Sci Educ. 19(2):ar22. doi: 10.1187/cbe.19-11-0235.
  • This article is not a primary literature publication, so it was not used in this annotation.

8.2. Main paper

  • Hinzke T, Kleiner M, Meister M, Schlüter R, Hentschker C, Pané-Farré J, Hildebrandt P, Felbeck H, Sievert SM, Bonn F, Völker U, Becher D, Schweder T, Markert S. 2021. Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis. Elife. 10:e58371. doi: 10.7554/eLife.58371.
  • This article is licensed for Creative Commons use using CC BY 4.0, which allows re-use and adaptation with proper attribution and notation of any changes. See https://elifesciences.org/articles/58371#copyright

License

Icon for the Creative Commons Attribution 4.0 International License

Podcast Annotation and Resources in Microbiology Copyright © 2025 by Rebecca Seipelt-Thiemann; Nancy Boury; Gwendowlyn S. Knapp; Amaya Garcia Costas; and Patrick Armstrong is licensed under a Creative Commons Attribution 4.0 International License, except where otherwise noted.

Share This Book