Microbial Ecology

TWiM #231: It’s a Microbe-Eat-Microbe World

Podcast and Annotation Information
  • Annotation by Katie Huber, Nick Karnyski, Jonelle Mattiacio
  • Podcast audio by TWiM: Listen to TWiM #231 Podcast
  • Podcast transcript by Otter.ai and edited by Laurel Thompson and Harshita Sharma: Access Podcast Transcripts
  • Papers Discussed:
    • Cockell CS, Santomartino R, Finster K, Waajen AC, Eades LJ, Moeller R, Rettberg P, Fuchs FM, Van Houdt R, Leys N, Coninx I, Hatton J, Parmitano L, Krause J, Koehler A, Caplin N, Zuijderduijn L, Mariani A, Pellari SS, Carubia F, Luciani G, Balsamo M, Zolesi V, Nicholson N, Loudon CM, Doswald-Winkler J, Herová M, Rattenbacher B, Wadsworth J, Craig Everroad R, Demets R. 2020. Space station biomining experiment demonstrates rare earth element extraction in microgravity and Mars gravity. Nat Commun. 11(1):5523. doi: 10.1038/s41467-020-19276-w.
    • Moreira D, Zivanovic Y, López-Archilla AI, Iniesto M, López-García P. 2021. Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii. Nat Commun. 12(1):2454. doi: 10.1038/s41467-021-22762-4.

1. Paper Abstracts

1.1. Snippet paper; discussion starts at 3:01 minutes

The Most Interesting Things (according to students)

We found the idea of bioleaching, the use of microorganisms to solubilize metals from solid materials very interesting. The bacteria produce organic acids and other compounds that help dissolve the metals, making them easier to extract. We thought that this was an interesting way to go about a commonly occurring problem. We have been extracting metals from earth for thousands of years and now we are able to use something as small as bacteria to do the work for us. This is also an environmentally friendly way to extract metals whereas other techniques can harm the environment.

“Microorganisms are employed to mine economically important elements from rocks, including the rare earth elements (REEs), used in electronic industries and alloy production. We carried out a mining experiment on the International Space Station to test hypotheses on the bioleaching of REEs from basaltic rock in microgravity and simulated Mars and Earth gravities using three microorganisms and a purposely designed biomining reactor. Sphingomonas desiccabilis enhanced mean leached concentrations of REEs compared to non-biological controls in all gravity conditions. No significant difference in final yields was observed between gravity conditions, showing the efficacy of the process under different gravity regimens. Bacillus subtilis exhibited a reduction in bioleaching efficacy and Cupriavidus metallidurans showed no difference compared to non-biological controls, showing the microbial specificity of the process, as on Earth. These data demonstrate the potential for space biomining and the principles of a reactor to advance human industry and mining beyond Earth.” (Cockell et al 2020, no changes)

1.2. Main paper; discussion starts at 31:26 minutes

The Most Interesting Things (according to students)

We found the discussion on Horizontal Gene Transfer (HGT) and CRISPR Systems very interesting.The podcast hosts discuss how CRISPR systems can be used to investigate past viral attacks by examining repeat sequences in microbial DNA. They also explore the presence of holin genes and genomic islands, suggesting horizontal gene transfer events and viral interactions in the evolutionary history of predatory bacteria.

“The Candidate Phyla Radiation (CPR) constitutes a large group of mostly uncultured bacterial lineages with small cell sizes and limited biosynthetic capabilities. They are thought to be symbionts of other organisms, but the nature of this symbiosis has been ascertained only for cultured Saccharibacteria, which are epibiotic parasites of other bacteria. Here, we study the biology and the genome of Vampirococcus lugosii, which becomes the first described species of Vampirococcus, a genus of epibiotic bacteria morphologically identified decades ago. Vampirococcus belongs to the CPR phylum Absconditabacteria. It feeds on anoxygenic photosynthetic gammaproteobacteria, fully absorbing their cytoplasmic content. The cells divide epibiotically, forming multicellular stalks whose apical cells can reach new hosts. The genome is small (1.3 Mbp) and highly reduced in biosynthetic metabolism genes, but is enriched in genes possibly related to a fibrous cell surface likely involved in interactions with the host. Gene loss has been continuous during the evolution of Absconditabacteria, and generally most CPR bacteria, but this has been compensated by gene acquisition by horizontal gene transfer and de novo evolution. Our findings support parasitism as a widespread lifestyle of CPR bacteria, which probably contribute to the control of bacterial populations in diverse ecosystems.” (Moreira et al 2021, no changes).

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

Snippet Main
Vision and Change Topics
  • Microbial Ecology (V&C_ME)
  • Impact of Microorganisms (V&C_IM)
  • Evolution (V&C_E)
  • Microbial Ecology (V&C_ME)
  • Structure and Function (V&C_SF)
ASM Fundamental Statements
  • Fundamental Statement 21 (ASM_21): Microbes and the environment interact with and affect each other.
  • Fundamental Statement 26 (ASM_26): Humans leverage microbes and their products to address problems and improve quality of life.
  • Fundamental Statement 27 (ASM_27): The extent of microbial diversity is largely unknown, and exploration of this diversity is critical to understanding microbes and their role in the biosphere
  • Fundamental Statement 3 (ASM_3): The evolution of microbes is impacted by their interactions with the environment and a variety of ecological forces, including other microbes, humans, and habitats.
  • Fundamental Statement 7(ASM_ 7): Microbes have evolved structures adapted for specific functions that are often associated with a fitness advantage in a particular environment.
  • Fundamental Statement 20 (ASM_20): Microbes are ubiquitous, found in diverse and dynamic ecosystems, where they use available resources and often form complex communities.

3.  Potential Learning Objectives for the Podcast

The student will be able to: Paper1 Order2
  • Identify the relationship between biomining and sustainability regarding rare earth metals.
  • Recall the bacterium that was found to be effective in biomining in micro-gravity.
 S L
  • Make conclusions on the bacterial effectiveness in extracting rare earth elements under various gravity conditions when given alternate results.
 S H
  • Recall characteristics that support Vampirococcus is a predatory bacterium and not a virus.
  • Identify the role of molecular factors in the ability of Vampirococcus lugosii to consume other bacteria.
  • Identify the prey of Vampirococcus lugosii.
 M L
  • Analyze an alternate, hypothetical interaction to identify the symbiotic relationship.
 M H

1 Papers: Snippet (S) or Main (M)

2 Learning 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

  • Biomining (8:45–17:15):  The process of using microorganisms to extract metals and rare earth minerals from ores and other solid materials. On the International Space Station (ISS) Sphingomonas desiccabilis, Bacillus subtilis, and Cupriavidus metallidurans were tested for efficiency of biomining under different gravity conditions: no gravity, Mars gravity, and Earth gravity.

4.2. Main Paper

  • Single-cell Genomics (21:24–25:10): This technique is one where single cell’s genome is used for next-generation sequencing to sequence the cell’s entire genome.
  • Micromanipulators (21:24; 43:52): These are tools used to move small things around.  Here they were used to isolate single cells for genomic analysis.
  • Scanning and Transmission Electron Microscopy (25:10; 29:26): Electron microscopy (EM) is a form of high resolution microscopy.  Scanning EM (SEM) uses an electron beam to scan a surface, and it was used to confirm the Vampirococcus epibiont status of outside the predation cell.  Transmission EM (TEM) is another form of high resolution microscopy that uses high energy electrons to examine internal structures in a sample and was used to identify the Vampirococcus membrane structure.

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

5.1. Snippet Paper

  • Biomining / Bioleaching (8:54–12:50): Sphingomonas desiccabilis can be used to extract rare earth elements (REE) at the International Space Station.

5.2. Main Paper

  • Candidate Phyla Radiation (CPR) (20:50–25:10):  A large supergroup of mostly uncultured bacteria discovered by metabarcoding and metagenomics in diverse environments, with small genome sizes, limited biosynthetic capabilities and thought to be symbionts of other organisms.
  • Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein (CRISPR/Cas) (33:39–35:53): Vampirococcus possess two bacterial defense systems called CRISPR-Cas systems that encode a number of proteins that may represent new effectors.

6. Podcast Questions

  1. Which bacterium was found to be effective in extracting rare earth elements in space conditions?
    1. Bacillus subtilis 
    2. Cupriavidus metallidurans 
    3. Sphingomonas desiccabilis 
    4. Escherichia coli
  2. How does biomining contribute to sustainability?
    1. It uses less energy and reduces the environmental impact.
    2. It decreases the need for toxic chemicals and machinery.
    3. It requires a large amount of water and results in less pollution.
    4. It decreases natural resources faster than traditional mining.
  3. The podcasters note which species was most effective at biomining, but do not discuss the results that provided evidence for this.  Let’s say that they incubated each species (or none) with a specific amount of mineralized rock and examined what rare earth metals remained in the mineralized rock after the incubation.  If their results had been those shown in the table, which species shows the best biomining?  What is your evidence?
    1. Bacillus subtilis;  this species has balanced recovery/utilized at 50%.
    2. Cupriavidus metallidurans; this species has the highest utilized value.
    3. Sphingomonas desiccabilis; this species a highest utilized value.
    4. Escherichia coli; this species has the highest recovered value of all.
Species Average percent recovered
No bacterium 98
Bacillus subtilis  50
Cupriavidus metallidurans  30
Sphingomonas desiccabilis  65
Escherichia coli 75
  1. What characteristics do the podcast speakers discuss that suggest Vampirococcus lugosii is not a virus? [pick all that apply]
    1. Is filterable at 0.2 microns
    2. Contains CRISPR elements
    3. Divides by assembly of components
    4. Lacks an electron transport system
    5. Contains DNA restriction systems
    6. Produces peptidoglycan
  2. What role do enzymes, receptors, or other cell surface factors play in Vampirococcus lugosii’s ability to consume other bacteria?
    1. They act as a defense mechanism, protecting V. lugosii from being neutralized or engulfed by other predators.
    2. They assist in the formation of biofilms, allowing V. lugosii to thrive in aerobic, nutrient-rich environments.
    3. They help V. lugosii break down complex sugars released into the environment by the prey bacterium.
    4. They facilitate the recognition and binding of V. lugosii as well as acquisition of cytoplasmic components.
  3. What type of bacteria were Vampirococcus lugosii prey?
    1. Chlamydia
    2. Rickettsia
    3. Halochromatium 
    4. Any bacteria in the lake
  4. If the researchers find that Vampirococcus interacts with another species, but it does not appear to degrade its interaction partner, what type of symbiosis would this be?
    1. Commensalism
    2. Parasitism
    3. Mutualism
    4. Amensalism

7. Figure Reading Exercises

The following are two figure reading exercises, both from the main paper (Figures 1; Figure 3).

7.1. First Figure Reading Exercise

7.1.1. Learning Objectives

Students will be able to: 

  • Identify the features of the environment in which Vampirococcus was found.
  • Identify the different microscopy techniques used to observe Vampirococcus cells
  • Analyze the evidence to make conclusions about Vampirococcus lifestyle features.
  • Propose an ecological role for Vampirococcus in its native environment.
Experimental Background (Moreira et al., Figure 1)

Candidate Phyla Radiation (CPR) are a large group of mostly uncultured bacterial lineages characterized by small cell sizes and limited biosynthetic capabilities. CPR bacteria are significant because they represent a substantial portion of bacterial diversity and play crucial roles in microbial ecosystems, potentially controlling bacterial populations. In an effort to characterize species present in extreme environments, Moreira et al. (2021) sampled the athalassic salt lake Salada de Chiprana, a land-locked lake with highly concentrated salt water and due to these conditions it contains thick microbial mats (panels a and b).  These mats cause the deepest parts of the lake to be anoxic, sulfide rich environments where sulfide-dependent anoxygenic photosynthetic bacteria can live. In their sampling, the researchers identified a new CPR bacterium of the phylum Absconditabacteria, which they named Vampirococcus lugosii. In this study, the authors sought to understand V. lugosii’s lifestyle and its ecological impact on bacterial communities. They first characterized how this very small bacterium interacted with larger anoxygenic photosynthetic bacteria using light microscopy (panels d-f).  They next used scanning electron microscopy, which captures surface images of samples, to examine the interaction at very high resolution (panel g).  They also used transmission electron microscopy, which captures images with information about internal structures of samples, to examine the interaction at very high resolution (panels h and i).

photos and microscopy images
Figure 1. “Sampling site and microscopy observation of Vampirococcus cells.. a General view of the microbial mat covering the shore of the Salada de Chiprana lake. b Closer view of a microbial mat section. c Natural population of blooming sulfide-dependent anoxygenic photosynthetic bacteria in waters of microbial mat containers after several weeks of growth in the laboratory; note the conspicuous refringent intracellular sulfur inclusions. d–f Closer microscopy view of anoxygenic photosynthetic bacteria infected by epibiotic Vampirococcus cells and few-cell filaments (indicated by yellow arrows). g Scanning electron microscopy image of a host cell infected by two stacking Vampirococcus cells (yellow arrow). h Transmission electron microscopy (TEM) image of a thin section of a host cell infected by Vampirococcus (yellow arrow). i Closer TEM view of a thin section of Vampirococcus cells, notice the fibrous rugose cell surface and the large space separating contiguous cells. Scale bars: 5 cm (b), 5 µm (c), 1 µm (d–h), 0.5 µm (i).” (Moreira et al. 2021, no changes)

7.1.2. Questions

  1. What microscopy techniques were used to observe Vampirococcus cells (panels c-i)? [pick all that apply]
    1. Light microscopy
    2. Fluorescence microscopy
    3. Scanning electron microscopy
    4. Transmission electron microscopy
    5. Atomic force microscopy
    6. Phase-contrast microscopy
    7. Dark-field microscopy
  2. What environmental conditions characterize the Salada de Chiprana lake, where Vampirococcus is found?
    1. Oxygen-rich, fast-moving freshwater streams
    2. Hypersaline, sulfidic waters with microbial mats
    3. Warm, volcanic, deep-sea hydrothermal vents
    4. Dry, high radiation level desert environments
  3. What evidence supports the hypothesis that Vampirococcus has an epibiotic lifestyle, that is it lives on the surface of other cells?
    1. The presence of a cross-linked peptidoglycan layer on Vampirococcus cells
    2. The presence of intracellular, crystalline sulfur granules in Vampirococcus cells
    3. The observation of Vampirococcus forming stalks and attaching to host cells
    4. The detection of multiple, highly structured flagella on Vampirococcus cells
  4. What evidence in the microscopic images suggests a mechanism that Vampirococcus lugosii uses to acquire nutrients from its host?
    1. Tight contact between cell surfaces, allowing nutrient absorption without entering the host
    2. The engulfment of the entire prey cell and subsequent complete digestion of the prey cell
    3. The needle-like structure which injects digestive enzymes directly into the host cytoplasm
    4. The fusion of the two bacterial membranes which then connects cytoplasmic contents
  5. What ecological role might Vampirococcus play based on the evidence in these microscopy data and the conclusions that can be made from them?
    1. Vampirococcus is a primary producer in microbial mats and functions in global carbon cycling.
    2. Vampirococcus controls bacterial populations by preying on anoxygenic photosynthetic bacteria.
    3. Vampirococcus contributes to nitrogen fixation in extreme, high-salinity aquatic ecosystems.
    4. Vampirococcus serves as a symbiotic partner providing an exchange of nutrients with hosts.

7.2. Second Figure Reading Exercise

7.2.1. Learning Objectives

Students will be able to:

  • Identify key features in the schematic/cartoon.
  • Identify a likely mechanism by which Vampirococcus cells attach to target host cells.
  • Hypothesize Vampirococcus’s level of independence based on the genes/functions encoded in its genome.
  • Predict how a small molecule inhibitor would affect specific Vampirococcus activities and what the outcome would be.
Experimental Background (Moreira et al., Figure 3)

Candidate Phyla Radiation (CPR) are a large group of mostly uncultured bacterial lineages characterized by small cell sizes and limited biosynthetic capabilities. CPR bacteria are significant because they represent a substantial portion of bacterial diversity and play crucial roles in microbial ecosystems, potentially controlling bacterial populations. In an effort to characterize species present in extreme environments, Moreira et al. (2021) sampled the athalassic salt lake Salada de Chiprana, a land-locked lake with highly concentrated salt water and due to these conditions it contains thick microbial mats where sulfide-dependent anoxygenic photosynthetic bacteria can live. In their sampling, the researchers identified a new CPR bacterium of the phylum Absconditabacteria, which they named Vampirococcus lugosii. In previous microscopic characterizations they showed that Vampirococcus cells attach to the host cell surface in a stacking formation, and kill it by consumption of its cytoplasmic content. Using micromanipulation techniques, the authors isolated individual Vampirococcus cells and performed single-cell genomics to characterize the genes present in this unusual species.  Metabolic and structural proteins encoded in the Vampirococcus genome are presented in the cartoon diagram of two stacked Vampirococcus cells preying on a host cell.

schematic/cartoon
Figure 3. “Metabolic and cell features inferred from the genes encoded in the Vampirococcus genome. The diagram shows the host cell surface (bottom) with two stacking Vampirococcus cells attached to its surface (as in Fig. 1h). “(Moreira et al. 2021, no changes)

7.2.2. Questions

  1. Generally, in a model figure, structures and color coding denotes something the authors wish to identify, highlight ,or summarize.  What function is indicated by the green oval and where is this protein’s location?
    1. Host cell; inner membrane
    2. Vampirococcus cell; cytoplasm
    3. Host cell; extracellular space
    4. Vampirococcus cell; membrane
  2. Based on the model figure, how do you think Vampirococcus cells attach to the host/prey cell surface? [pick all that apply]
    1. Type IV pili
    2. Membrane ATPase
    3. Giant surface proteins
    4. ABC transporter (iron)
    5. Sulfate permease
  3. There are three red circles with slashes through them along with three phrases at the center of the bottom Vampirococcus cell.  What do these indicate and what does this information imply about the host-predator relationship?
    1. Missing pathway; Vampirococcus must rely on the prey/host for these molecules.
    2. Transporter function; Vampirococcus can produce these molecules independently.
    3. Murein biosynthesis; Vampirococcus acquired these genes from the host/prey cell.
    4. Antiporter function; Vampirococcus synthesizes ATP reversing its proton motive force.
  4. If you were to create a small molecule inhibitor of ComEA/ComEC transporters, which vital function would be affected in Vampirococcus, and what would the outcome be for Vampirococcus?
    1. Ability to import proteins; Vampirococcus would be unable to synthesize proteins.
    2. Ability to import RNA; Vampirococcus would be unable to transcribe its genome.
    3. Ability to import DNA; Vampirococcus would be unable to replicate its own DNA.
    4. Ability to import lipids; Vampirococcus would be unable to make cell membranes.

8. Paper Information and Licensing

8.1. Snippet paper

  • Cockell CS, Santomartino R, Finster K, Waajen AC, Eades LJ, Moeller R, Rettberg P, Fuchs FM, Van Houdt R, Leys N, Coninx I, Hatton J, Parmitano L, Krause J, Koehler A, Caplin N, Zuijderduijn L, Mariani A, Pellari SS, Carubia F, Luciani G, Balsamo M, Zolesi V, Nicholson N, Loudon CM, Doswald-Winkler J, Herová M, Rattenbacher B, Wadsworth J, Craig Everroad R, Demets R. 2020. Space station biomining experiment demonstrates rare earth element extraction in microgravity and Mars gravity. Nat Commun. 11(1):5523. https://doi.org/10.1038/s41467-020-19276-w
  • 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. Please see https://www.nature.com/articles/s41467-020-19276-w#rightslink

8.2. Main paper

License

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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.

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