Microbial Ecology

TWiM #261: Overwhelming Microbial Greatness

Podcast and Annotation Information
  • Annotation by Jenny Stovall, Briana Lanzarotta, Luke Boseman, Nicole L. Podnecky and Angela Wilson.
  • Podcast audio by TWiM: Listen to TWiM #261 Podcast
  • Podcast transcript by Otter.ai and edited by Marvin Romo and Grace Helle: Access Podcast Transcripts
  • Papers Discussed:
    • Coban O, De Deyn GB, van der Ploeg M. 2022. Soil microbiota as game-changers in restoration of degraded lands. Science. 375(6584). doi: 10.1126/science.abe0725
    • Volland J, Gonzalez-Rizzo A, Gros O, Tyml T, Ivanova N, Schulz F, Goudeau D, Elisabeth N, Nath N, Udwary D, Malmstrom RR, Guidi-Rontani C, Bolte-Kluge S, Davies KM, Jean MR, Mansot J-L, Mouncey NJ, Angert ER, Woyke T, Date SV. 2022. A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles. Science. 376(6600): 1453-1458. doi: 10.1126/science.abb363

1. Paper Abstracts

1.1. Snippet paper; discussion starts at 2:26 minutes

The Most Interesting Things (according to students)

It is found it interesting just how much soil is being discarded into the oceans. The podcast mentions how 24 billion metric tons of soil is being lost every year. The fact that 0.05% of freshwater is needed to support life on land is such a minimal percentage but crucial for survival is crazy. Before listening to this episode, I didn’t realize just how important diverse microbial communities are for keeping soil healthy. Usually, when we think about soil quality, we think of things like fertilizer, worms, and water—not microbes. But this podcast really opened my eyes to how essential those tiny organisms are for soil maintenance and health. Plus, the idea that we might be able to tweak or manage these microbes to help restore land is actually pretty interesting.

The abstract cannot be copied due to licensing restrictions. Please see licensing information and links to the article at the journal’s web page and/or PubMed in Section 8.1.

1.2. Main paper; discussion starts at 36:30 minutes

The Most Interesting Things (according to students)

It is interesting how this bacteria can be so large in size and yet it uses multiple strategies to thrive. For instance, the podcast discusses how this bacteria uses its large vacuole to store nitrate. I also find it interesting that you can see this bacteria with the naked eye. The size of the genome of this bacteria is interesting. Given that this bacteria is 1cm long, I had an understanding that it would have a high number of genome copies, but seeing that this unicellular bacteria has almost 37,000 genome copies was very surprising.

The abstract cannot be copied due to licensing restrictions. Please see licensing information and links to the article at the journal’s web page and/or PubMed in Section 8.1.

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)
  • Structure and Function (V&C_SF)
  • Metabolic Pathways (V&C_MP)
ASM Fundamental Statements
  • Fundamental Statement 12 (ASM_12): Bacteria and Archaea exhibit extensive metabolic diversity, including nitrogen fixation, methane production, and anoxygenic photosynthesis, many of which are unique to these two domains.
  • 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 21 (ASM_21): Microbes and the environment interact with and affect each other.
  • Fundamental Statement 24 (ASM_24): Microbes and their communities are essential for supporting all life as we know it.
  • Fundamental Statement 8 (ASM_8): Microbes have unique genomes, structures, and/or biochemical characteristics that distinguish them from each other.
  • Fundamental Statement 12 (ASM_12): Bacteria and Archaea exhibit extensive metabolic diversity, including nitrogen fixation, methane production, and anoxygenic photosynthesis, many of which are unique to these two domains.
  • Fundamental Statement 13 (ASM_13): Intrinsic factors, such as genotype, metabolism, and cell structures, impact the survival and growth of microbes.

3.  Potential Learning Objectives for the Podcast

The student will be able to: Paper1 Order2
  • Define the microbial diversity in the context of soil ecosystems.
  • Identify key roles of soil microbiota in maintaining soil structure and function.
 S L
  • Evaluate how microbial community changes can impact soil health and restoration outcomes.
 S H
  • Describe the structural features of Ca. Thiomargarita magnifica.
  • Recall how features of the large bacteria help it overcome physical and metabolic constraints.
  • Compare and contrast the genomic and structural features of giant bacteria with typical prokaryotes.
 M L
  • Design an experiment to determine whether the putative Ca. Thiomargarita magnifica secondary metabolite-like genes produce an antimicrobial compounds
 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

  • Metagenomic Sequencing (6:15 – 8:45; 9:00 –11:30; 19:26–20:00): This is a next generation sequencing technique that uses environmental DNA as a template in polymerase chain reaction to amplify  DNA sequences in bulk.  The DNA fragments are sequenced and compared to a database to identify the species present.  Here it was used to identify the species present and assess the composition of soil microbial communities.
  • Applied Microbiology (16:56–17:00; 29:30–32:31): These are methods used in applying microbiology solutions to world problems.  They discussed the use of microbes to assist in land restoration and affect the properties of the soil or populate regions which have too high salinity.

4.2. Main Paper

  • Fluorescence, X-ray and Electron Microscopy (42:00 – 42:24): These are a variety of microscopy techniques.  Here, they were used to visualization and characterize large bacteria.

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

5.1. Snippet Paper

  • Soil Conservation & Ecology (7:46–10:10; 11:22 -16:40): This snippet discussed the importance of soil conservation in regards to the microbiota that inhabit it. As soil is disposed of, the environment is affected by it.
  • Rhizobacteria & Microbial Soil Ecology (17:30–23:00): A number of microorganisms were briefly described and their roles in nutrient cycling and soil biology including plants, algae, archaea, bacteria, and protists.
  • Fungal Biology (22:20–23:00): Structure and function of hyphae & resistance to desiccation were discussed.
  • Bacterial Cell Walls (23:02–27:31): Gram positives (monoderms) and Gram negatives (biderms with LPS) were described.
  • Bacterial Phyla (23:45–24:54) Actinobacteria, Chloroflexi, and Firmicutes were mentioned as well as important roles these microbes play.

5.2. Main Paper

  • Sulfur-Reduction (37:04–38:36): Fermentation and hydrogen sulfide production were discussed.
  • Intracellular Compartments & Organelles (42:31–50:20): Vacuoles, membrane-bound compartments & ribosomes were discussed.
  • Metabolism (48:23–52:00): TCA, glycolysis, nitrogen metabolism and using nitrogen as a terminal electron acceptor were discussed.
  • Antimicrobial Properties (49:29–50:20): Antimicrobial compounds, type IV and type VI secretory systems were mentioned.
  • Cell Division & Structure (50:20–53:12; 59:07–59:49): Cell division was briefly discussed for this organism which more closely resembles spore formation or budding.
  • Protein Secretion (57:37–58:34): SecA was mentioned in the context of secreting pepin proteins.
  • Viral Evolution & RNA World (1:07:45–1:09:39): Virus capsids and bacteriophages were briefly discussed.

6. Podcast Questions

  1.  According to the podcast, what types of organisms contribute to microbial diversity in soil?
    1. Only bacteria and viruses.
    2. Only fungi and archaea.
    3. Archaea, bacteria, fungi, protists, and viruses.
    4. Plants, nematodes, worms and arthropods.
  2. What is one key ecological role of soil microbiota discussed in the podcast snippet?
    1. Regulation of weather patterns
    2. Degradation of soil structure
    3. Improvement of nutrient cycling
    4. Reduction of microbial populations
  3. In what way can manipulated soil microbiota benefit land use?
    1. Decrease oxygen levels in soil.
    2. Accelerate restoration of degraded lands.
    3. Destroy weedy plant root systems.
    4. Replace chemical fertilizers entirely.
  4. What unique structural feature occupies most of the volume inside Ca. Thiomargarita magnifica?
    1. Pepins
    2. Multiple cell walls
    3. Central vacuole
    4. Ribosomes
  5. Why is it beneficial for Ca. Thiomargarita magnifica to contain tens of thousands of genome copies?
    1. To mimic the  spatial organization of a eukaryotic nucleus.
    2. To compensate for the reduced ratio of ribosomes to mRNA.
    3. To maintain the external shape of the much elongated cell wall.
    4. To distribute transcription and translation across the large cell.
  6. Which of the following is not a typical feature of most prokaryotes, but is seen in Ca. Thiomargarita magnifica?
    1. Monodermal cell without peptidoglycan
    2. Membrane-bound compartments
    3. A circular genome
    4. Lack of SecA proteins
  7. The podcasters note that when the researchers identified genes in the Ca. Thiomargarita magnifica genome, they found secondary metabolite-like genes that resemble antimicrobial synthesis genes. How could you determine whether Ca. Thiomargarita magnifica produce antimicrobial compounds?
    1. Use mass spectrometry to identify proteins.
    2. Use a spectrophotometer to measure cell density.
    3. Use a variation of the antibiotic disk diffusion assay.
    4. Use fluorescent microscopy to examine membranes.

7. Figure Reading Exercises

The following are two figure reading exercises, one from the snippet paper (Figure 4) and one from the main paper (Figure 3A).

7.1. First Figure Reading Exercise

7.1.1. Learning Objectives

Students will be able to:

  • Identify healthy soil and degraded soil features.
  • Identify the effects of increased vs decreased drainage of soils.
  • Predict soil health when given a specific soil measure.
  • Infer how soil measures are affected by microbes with specific features.
Experimental Background (Coban et al., Figure 4)

Soils play an important part in the Earth’s ecosystems, including filtering water, as well as providing growth medium and habitats for plants and microbes.  Soil degradation is a major concern because soils are such an integral piece of energy and nutrient cycling.  In this review by Coban et al (2022), the authors review and consolidate experimental evidence on how soil loss, loss of chemical properties, and contamination impact by microorganisms. They focus on the effect of microorganisms on soil hydraulics, that is, how water moves through the soil. Soil hydraulics measures include: 1) aggregate stability (how well soil clumps), 2) the structure of the soil (arrangement of clumps), and 3) the organic matter present and microtopography (small bumps, ridges and other topography of the surface of the soil). From these observations, investigators can better understand water absorption, seepage, retention, and drainage. This schematic shows a comparison of soil hydraulics (blue icons) and the microbiota (bacteria & fungi in circular insets) within healthy soil (left side, orange) and degraded soil (right side, yellow).

  • The figure cannot be copied due to licensing restrictions. Please see licensing information and links to the article at the journal’s web page and/or PubMed in Section 8.1.

7.1.2. Questions

  1. Which of the following are affected by soil degradation? [pick all that apply]
    1. Water infiltration
    2. Microbial communities
    3. Drainage and seepage
    4. Uptake by roots
  2. An increase in drainage is an indicator that the soil is __________ .
    1. healthy
    2. degrading
    3. recovering
    4. unaffected
  3. An increase in the number or diversity of microbes found in the soil would indicate that the soil is becoming                         .
    1. resistant to recovery
    2. sensitive to infiltration
    3. sensitive to puddling
    4. less degraded (healthy)
  4. Why would a degraded soil have a decrease in the amount of water it can hold?
    1. Decreased microbial communities, EPSs, and soil organic matter
    2. Increased microbial communities and EPSs and decreased soil matter
    3. Decreased microbial communities and increased soil matter and EPSs
    4. Decreased microbial communities and EPSs and increased soil matter

7.2. Second Figure Reading Exercise

7.2.1. Learning Objectives

Students will be able to:

  • Identify features of phylogenetic trees, bar graphs, and pattern data.
  • Describe the genome of Ca. Thiomargarita magnifica.
  • Compare the genomes of Ca. Thiomargarita spp. and other related organisms.
  • Analyze the data provided to make conclusions about the relatedness, ploidy, and size of organisms.
Experimental Background (Volland et al., Figure 3A)

Bacteria are widely known to be microscopic organisms, but one recently-discovered species of bacteria has sparked curiosity as to whether larger bacteria exist. In Volland et al (2022) the authors investigate and characterize an atypical, novel species of bacteria. Formally known as the Thiomargarita bacteria, Candidatus Thiomargarita magnifica is drastically larger in size than all known bacteria. Ca. T. magnifica and other “giant bacteria” are polypoid meaning they contain multiple copies of the genome, which is often correlated with the accumulation of redundant biosynthetic pathway genes. Here, Volland et al (2022) used whole genome sequencing and bioinformatics to establish and analyze a near complete genome for Ca. T. magnifica isolated from a sunken leaf.  To compare this genome to related species, the authors clustered sequences representing 56 protein coding genes each and produced a phylogenetic tree (panel A, left).  Genome quality and confidence (branch support/bootstrap values) are indicated by colored circles. The assembled genome size (assembly size), completeness (% completeness), number of predicted protein coding sequencing (CDS), and proportion of CDS predicted to be biosynthetic gene clusters (BCGs) was determined and compared to the other taxonomically-related large bacteria. Because these are large bacteria, the researchers also identified patterns in cell division “gene group” completeness (panel A; right side; pattern 1) and duplication in genes related to cell elongation (panel A; right side; pattern 2).

  • The abstract and figures cannot be copied due to licensing restrictions. Please see licensing information and links to the article at the journal’s web page and/or PubMed in Section 8.1.

7.2.2. Questions

  1. What does the red color circle for Ca. Thiomargarita nelsonii bud S10 in the phylogenetic tree data indicate?
    1. The genome quality is unknown.
    2. The genome is high quality.
    3. The genome is moderate quality.
    4. The genome is low quality.
  2. Rank the following organisms in order of most related to most distant from Ca. T. magnifica.
W:  Ca. Maithrix sp. Canyon 246
Y:  Ca. Thimargarita sp. Thio36
X:   Achromatium sp. WMS3
Z:  Thioploca ingrica Lake Okotanpe

Most closely  →  Most distantly

    1. Y … W … X … Z
    2. W … Y … Z … X
    3. Y … W … Z … X
    4. X … Z … W … Y
  1. Which of the following is/are true about the genome of Ca. T. magnifica? [pick all that apply]
    1. Less than 20% of its genes are biosynthetic cluster genes.
    2. It contains over 10,000 protein coding regions (CDS).
    3. The genome is predicted to be about 86.5% complete.
    4. The genome length is about double Ca. T. sp. Thio36.
  2. Which organism has the smallest number of coding regions?
    1. Ca. Marithrix sp. Canyon 246
    2. Ca. Thiomargarita sp. Thio36
    3. Achromatium sp. WMS3
    4. Beggiatoa sp. PS
  3. Based on its CDS count and proportion of BGCs, which of the following organisms is most likely to be polyploid?
    1. Achromatium sp. WMS3
    2. Beggiatoa alba B18LD
    3. Ca. Marithrix sp. Canyon 24
    4. Ca. Thiomargarita sp. Thio36
  4. What does Ca. Thiomargarita magnifica’s pattern of cell division and cell elongation genes suggest?
    1. The lack of cell division genes along with duplication in cell elongation genes suggests the cells will be big.
    2. The presence of cell division genes along with duplication in cell elongation genes suggests the cells will be small.
    3. The lack of cell division genes along with deletion in cell elongation genes suggests the cells will be large and round.
    4. The presence of cell division genes along with deletion in cell elongation genes suggests the cells will be round.

8. Paper Information and Licensing

8.1. Snippet paper

  • Coban O, De Deyn GB, van der Ploeg M. 2022. Soil microbiota as game-changers in restoration of degraded lands. Science. 375(6584). doi: 10.1126/science.abe0725
  • This article is not licensed for Creative Commons use. Thus, the abstract and figures cannot be copied here. Please see the article at the journal’s web page.

8.2. Main paper

  • Volland J, Gonzalez-Rizzo A, Gros O, Tyml T, Ivanova N, Schulz F, Goudeau D, Elisabeth N, Nath N, Udwary D, Malmstrom RR, Guidi-Rontani C, Bolte-Kluge S, Davies KM, Jean MR, Mansot J-L, Mouncey NJ, Angert ER, Woyke T, Date SV. 2022. A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles. Science. 376(6600): 1453-1458. doi: 10.1126/science.abb363
  • This article is not licensed for Creative Commons use. Thus, the abstract and figures cannot be copied here. Please see the article at the journal’s web page.

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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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