Evolution

TWiM #248: Borgs are Real

Podcast and Annotation Information

  • Annotation by Saniya Barkat, Priyanka Bhatt, Sofie Kupiec, Adam Nuevo, Jeremy T. Ritzert, and Rebecca Seipelt-Thiemann
  • Podcast audio by TWiM: Listen to TWiM #248 Podcast
  • Podcast transcript by Otter.ai and edited by Saniya Barkat, Priyanka Bhatt, Sofie Kupiec, Adam Nuevo, and Marvin Romo: Access Podcast Transcripts
  • Papers Discussed:
    • Peifer M. 2021. Looking back on a life of unacknowledged privilege and a call to action. Mol Biol Cell. 2021 32(11):1081-1085. doi: 10.1091/mbc.E21-01-0024.
    • Al-Shayeb B, Schoelmerich MC, West-Roberts J, Valentin-Alvarado LE, Sachdeva R, Mullen S, Crits-Christoph A, Wilkins MJ, Williams KH, Doudna JA, Banfield JF. 2022. Borgs are giant genetic elements with potential to expand metabolic capacity. Nature. 610(7933):731-736. doi: 10.1038/s41586-022-05256-1

1. Paper Abstracts

1.1. Snippet paper; discussion starts at 2:46 minutes

The Most Interesting Things (according to students)

The impact of barriers, opportunities, and mentorship on student learning was interesting.

“The year 2020 provided a wake-up call about the role systemic racism plays in shaping our nation and shaping science. While hard work and great mentors helped bring me a long way from a farm in Minnesota, it’s become much clearer that the privilege of being white and male and the accumulated advantages that began there played powerful roles. It’s time for white scientists like me to listen, think, and take action. We all have personal stories that we use to describe our trajectory in life and science. For the past five decades the narrative I told myself was a simple one of good luck, hard work, support from my community, and mentors at pivotal times. However, in many important ways, this was just a small part of the truth, ignoring the role unperceived privilege played. The many underlying injustices that were laid bare in our nation this past year began to open my eyes, prompting me to look back at the roles hidden privilege played in my career and the power that these have given me. This challenged me to use the power of that privilege to speak and act to try to change the system in which engrained advantages benefit some but not all. I am telling my story in hopes it will encourage my white colleagues to examine their own.” (Peifer 2021).

1.2. Main paper; discussion starts at 26:52 minutes

The Most Interesting Things (according to students)

Microbes undergo horizontal gene transfer to allow them to evolve without any potential evolutionary costs.

“Anaerobic methane oxidation exerts a key control on greenhouse gas emissions1, yet factors that modulate the activity of microorganisms performing this function remain poorly understood. Here we discovered extraordinarily large, diverse DNA sequences that primarily encode hypothetical proteins through studying groundwater, sediments and wetland soil where methane production and oxidation occur. Four curated, complete genomes are linear, up to approximately 1 Mb in length and share genome organization, including replichore structure, long inverted terminal repeats and genome-wide unique perfect tandem direct repeats that are intergenic or generate amino acid repeats. We infer that these are highly divergent archaeal extrachromosomal elements with a distinct evolutionary origin. Gene sequence similarity, phylogeny and local divergence of sequence composition indicate that many of their genes were assimilated from methane-oxidizing Methanoperedens archaea. We refer to these elements as ‘Borgs’. We identified at least 19 different Borg types coexisting with Methanoperedens spp. in four distinct ecosystems. Borgs provide methane-oxidizing Methanoperedens archaea access to genes encoding proteins involved in redox reactions and energy conservation (for example, clusters of multihaem cytochromes and methyl coenzyme M reductase). These data suggest that Borgs might have previously unrecognized roles in the metabolism of this group of archaea, which are known to modulate greenhouse gas emissions, but further studies are now needed to establish their functional relevance.” (Al-Shayeb et al. 2022)

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

Snippet Main
Vision and Change Topics
  • n/a
  • Metabolic Pathways (V&C_MP)
  • Information Flow and Genetics (V&C_IFG)
  • Evolution (V&C_E)
ASM Fundamental Statements
  • n/a
  • Fundamental Statement 2 (ASM_2): The diversity of microbes has arisen because of processes that include horizontal gene transfer, mutation, reassortment, recombination, and natural selection in varying ecological niches favor the growth and survival of certain variants.
  • 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.

3.  Potential Learning Objectives for the Podcast

The student will be able to: Paper1 Order2
  • n/a
 S L
  • n/a
 S H
  • Identify examples of key concepts from the paper discussion.
  • Identify the arguments that support that Borg elements are not located within an archaeal genome.
  • Identify how horizontal gene transfer, with selective pressure, can affect fitness.
 M L
  • Hypothesize the relationship between Borg elements and the environments from which they might be isolated in future studies.
 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

  • n/a

4.2. Main Paper

  • Filtration (33:41–33:54; 34:30–34:41): Scientists used a custom-built filtration system to filter groundwater to capture environmental DNAs which they analyzed by sequencing and identified unique extrachromosomal DNA fragments.
  • Deep Sequencing/High Throughput Sequencing (33:54–35:06): This technique is a variation of next-generation sequencing where researchers generate a considerable amount of sequence data to get “high coverage” of the sequences in a sample. This allows researchers to identify rare sequences and have high confidence. Here, the researchers used this method with environmental DNA captured from the subsurface anaerobic environment in Rifle, Colorado and the wetlands of California.
  • Mass Spectrometry (38:54–39:17): This is a technique that uses mass and charge ratios to identify and quantify molecules in a mixture. Here, the podcasters discuss how another study that paralleled this study used this technique to analyze isotopic ratio of sulfur in microbial fossils.
  • Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) (44:27–44:58): This is a microbial defense against foreign DNA that is being used as a genome editing tool. This type of bacterial defense might be effective against the “Borgs.”

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

5.1. Snippet Paper

  • n/a

5.2. Main Paper

  • Microbial Genetics (29:04–29:21; 36:59–37:05): The microbes discovered use non-Darwinian evolution with genetic recombination and 23 borg-ish sequences.
  • Borg Discovery (33:38–33:58): A Custom-built filtration apparatus recovered biomass in 400 to 1200 Liters of groundwater which was then deep sequenced to identify large DNA elements with genes from archaea. The researchers called them “Borg” after the science fiction characters on Star Trek, The Next Generation because they “assimilate” genes from archaea.
  • Evolution and Fitness (34:40–36:23): The microbes discovered use horizontal gene transfer and carry large amounts of DNA to adapt to their environment.
  • Metabolism (40:48–41:20): The microbes discovered gained the ability to use methane oxidation.

6. Podcast Questions

  1. Which of the following are examples of horizontal gene transfer? [pick all that apply]
    1. A DNA element from one species is present in the genome of another distinct species.
    2. A low copy plasmid is transferred from one bacterium to another bacterium via conjugation.
    3. A bacteriophage transfers a gene to a new host genome that was present in a previous host.
    4. A CRISPR complex engages in a defense function against a specific bacteriophage.
  2. What was the evidence that the Borg elements are independent of the archaeal genome? [pick all that apply]
    1. They have genes encoding capsid proteins.
    2. They have complete genomes that are linear.
    3. They have different genes than archaea.
    4. They are culturable while archaea aren’t.
    5. They have inverted repeats at their ends.
  3. What role does the environment play in fitness as it relates to horizontal gene transfer?
    1. If a gene acquires a mutation that causes increased activity in a particular environment then fitness increases.
    2. If a gene is acquired that enhances survival or reproduction in a particular environment then fitness is increased.
    3. If a gene acquires a mutation that causes loss of function in a particular environment then fitness decreases.
    4. If a DNA element is acquired that increases genome size then fitness is decreased regardless of the environment.
    5. If a gene is acquired from the environment then fitness is increased regardless of the organism’s current environment.
  4. If you were to isolate environmental DNA from another environment, would you expect to find the same Borg elements?  Why or why not?
    1. Yes; like bacteriophage and bacteria “partners,” these are likely abundant in all environments.
    2. Yes; it is likely that the Borg elements are actually bacteriophages and infect bacteria not archaea.
    3. No; it would be unlikely to find any Borg elements since archaea are ammonia-oxidizing anaerobes.
    4. No; they will likely be different and the genes they contain would be based on the environment.

7. Figure Reading Exercises

The following are two figure reading exercises, both from the main paper (Figures 2 and 3).

7.1. First Figure Reading Exercise

7.1.1. Learning Objectives

Students will be able to:

  • Identify key features of violin plots, correlation matrix heat maps, and/or bar graphs related to this study.
  • Evaluate evidence and make conclusions about whether Borg elements are located within or external to an archaeal genome.
  • Evaluate evidence and make conclusions about whether Borg elements are related to each other and to Methanoperedens.

Experimental Background (Al-Shayeb et al., Figure 2a-c)

Horizontal gene transfer is a major driver of microbial evolution.  The main three mechanisms by which microbes can acquire exogenous genetic material, such as genes that confer resistance or new metabolic capacities, are transformation, conjugation, and transduction.  Studying genomes from environmental sources can provide valuable information related to these types of events and selection pressures microbes in specific environments encounter.  In this study, Al-Shayeb et al. (2022) isolated and sequenced environmental DNAs from environments conducive to anaerobic methane oxidation, which is important because methane oxidation is a key control point for greenhouse gas levels.  Among the sequences they identified were four complete linear DNA elements. The researchers named these linear extrachromosomal elements (ECE) as Borgs. They also identified fifteen other incomplete Borgs.  They designate all Borg elements by color names.  To identify the origin of the Borg sequences, the researchers compared the Borg sequences to genomes of known organisms to identify nearest relatives, but also characterize distinct Borg features.  They found that Borg elements have the capability to encode proteins and likely originate from and/or coexist as extrachromosomal fragments in unculturable methanotrophic archaea, Methanoperedens.  The researchers examined a variety of evidence to show similarity and distinctness between the archaea and the Borg including GC content (panel a), correlation of sequence mapping (panel b), and gene frequency by functional category (panel c).

Heat map and bar chart of results described in caption.
Figure 2. ”Borg and Methanoperedens spp. genomic features and abundance patterns. a, The average genome GC contents of Borgs and Methanoperedens spp. are distinct. The black line denotes the median, and the dashed lines show the interquartile range. b, Groups of related Methanoperedens spp. (rows) correlate with groups of Borgs (columns) across a set of 50 samples. The asterisks indicate two-sided Pearson correlations above 0.92 with FDR-corrected P values below 2.0 × 10–20 that suggest that Brown, Green, Orange, Beige and Ochre Borgs associate with one group of Methanoperedens spp., Olive, Cyan, Gold, Apricot and Rose associate with a second group, and Black associate with a third group.Black asterisks indicate best association with a Methanoperedens genome (correlation ≥ 0.92, P ≤ 1 × 10–20); grey asterisks indicate association with a scaffold containing the Methanoperedens L11 marker gene (correlation ≥ 0.92, P ≤ 1 × 10–20). c, Frequency of genes in different functional groups in the four complete Borg genomes….” (Al-Shayeb et al. 2022, figure text and images cropped to include panels a-c). Source: https://www.nature.com/articles/s41586-022-05256-1

7.1.2. Questions

  1. The frequency of the functions encoded by genes in the four complete Borg genomes are shown in panel c. Which function is quantified by the letter J?
    1. Phosphodiesterases
    2. Protein processing and transport
    3. Stress and environmental response
    4. Isoprenoid biosynthesis
  2. The frequency of the functions encoded by genes in the four complete Borg genomes are shown in panel c.  Which biological functions are most commonly encoded in Borg genomes (other than unknown)?
    1. Protein processing and transport
    2. DNA and RNA manipulation
    3. Central carbon metabolism
    4. Benzoate degradation
  3. The frequency of the functions encoded by genes in the four complete Borg genomes are shown in panel c.  What does the pattern of function frequencies indicate about the relationship of Borg genomes?
    1. They tend to encode similar functions and in similar frequencies, so are likely related to each other.
    2. They tend to encode all necessary functions for metabolism, cellular structure, and gene expression.
    3. They do not encode similar functions as each other and likely work symbiotically inside the archaea.
    4. They encode overlapping but very distinct functions indicating a level of Borg specialization.
  4. As part of their analysis, the researchers quantified the Guanine:Cytosine content of Borg elements in comparison to the Guanine:Cytosine content of Methanoperedens species (panel A). What conclusion can you draw from these data?  What is your evidence?
    1. They are alike because both contain Guanosine and Cytosine in their genomes.
    2. They are different; Borg genomes are smaller than Methanoperedens genomes.
    3. They are similar in their Guanosine:Cytosine content with both being < 50% G+C.
    4. They are distinct because Borg and Methanoperedens have different G+C content.
  5. As part of their analysis, the researchers correlated the sequencing reads mapped to Borg elements and the sequencing reads mapped to different Methanoperedens species (panel B). Here, correlation values range from 0 to 1.0.  What would a correlation of 0.95 indicate and what color would the block be?
    1. The specific Borg and the specific Methanoperedens species are very alike; pale blue
    2. The specific Borg and the specific Methanoperedens species are somewhat alike; teal blue
    3. The specific Borg and the specific Methanoperedens species are as alike as different;  blue
    4. The specific Borg and the specific Methanoperedens species are very different;  dark blue
  6. As part of their analysis, the researchers correlated the sequencing reads mapped to Borg elements and the sequencing reads mapped to different Methanoperedens species (panel B). Three groups of Borg appear to be highly similar in their read mapping to three groups of Methanoperedens species. Match the Borg group with their likely related Methanoperedens species group.
Borg Group Methanoperedens Species Group
________ Group 1: Olive, Cyan, Gold, Apricot, Rose Group a: Mp_44_31, Mp_44_15, Mp_43_19, Mp_44_135, Mp_44_10, Mp_44_9
________ Group 2: Black, Pink Group b: Mp_41_6, Mp_41_19, Mp_40_9, Mp_45_10, Mp_41_8, Mp_43_25, Mp_41_17, Mp_43_12, Mp_43_37, Mp_44_19, Mp_43_82
________ Group 3: Purple, Brown, Beige, Green, Orange, Ochre, Sky Group c: Mp_45_49, Mp_44_27, Mp_42_6, Mp_42_7, Mp_37_20, Mp_41_45, Mp_42_7, Mp_40_14, Mp_44_5

7.2. Second Figure Reading Exercise

7.2.1. Learning Objectives

Students will be able to:

  • Identify key features in the schematic model diagram for this study.
  • Identify the likely physical relationship between the Lilac Borg and Methanoperedens archaea.
  • Predict how an intracellular Lilac Borg might affect fitness if acquired by a host.

Experimental Background (Al-Shayeb et al., Figure 3)

Horizontal gene transfer is a major driver of microbial evolution.  The main three mechanisms by which microbes can acquire exogenous genetic material, such as genes that confer resistance or new metabolic capacities, are transformation, conjugation, and transduction.  Studying genomes from environmental sources can provide valuable information related to these types of events and selection pressures microbes in specific environments encounter.  In this study, Al-Shayeb et al. (2022) isolated and sequenced environmental DNAs from environments conducive to anaerobic methane oxidation, which is important because methane oxidation is a key control point for greenhouse gas levels.  Among the sequences they identified were four complete linear DNA elements. The researchers named these linear extrachromosomal elements (ECE) as Borgs, which they designate by color names.  Here, the researchers show their analysis of the Lilac Borg genome with a focus on the relationship of the genes encoded in the Lilac Borg genome that provide functional capacities to the methanotrophic archaea Methanoperedens, which is the putative source of these DNA elements,

Extracellular electron transfer process visualized.
Figure 3. “Cell cartoon illustrating capacities inferred to be provided to Methanoperedens spp. by the coexisting Lilac Borg. Like all Borgs, this Borg lacks the capacity for independent existence, and we infer that it replicates within host Methanoperedens spp. cells. Borg-specific proteins are those that were not identified in the genome of coexisting Methanoperedens spp. Borg-encoded capacities are grouped into the major categories of energy metabolism (including the MCR complex involved in methane oxidation), extracellular electron transfer (including MHCs) involved in electron transport to external electron acceptors, central carbon metabolism (including genes that enable production of polyhydroxybutyrate (PHB)) and stress response/defence (including production of compatible solutes). Locus codes are listed in Supplementary Table 7.” (Al-Shayeb et al. 2022)
7.2.2. Questions
  1. Which color denotes molecules in the figure that are Borg-specific?
    1. Molecules noted in dark orange
    2. Molecules noted in blue
    3. Molecules noted in gold
    4. Molecules noted in tan
  2. Which molecules in the figure are present in the Lilac Borg?
    1. Molecules noted in dark orange
    2. Molecules noted in blue
    3. Molecules noted in gold
    4. Molecules noted in tan
    5. All of the above
  3. Based on the metabolism molecules noted in the Lilac Borg, would you predict exist independently? What is your reasoning?
    1. Yes, they have established a symbiotic, but independent relationship with the archaea.
    2. No, they lack genes to encode all necessary metabolism and structures for independence.
    3. Yes, they encode a variety of energy production and other proteins for independence.
    4. No, they do not have any genomic components with which to encode necessary genes.
  4. How might acquisition of the Lilac Borg affect fitness of a host in an anaerobic environment?
    1. Increase by making the host more virulent and able to increase doubling rates.
    2. Decrease by adding to the cost and time to the complete DNA replication.
    3. Increase by providing more proteins in redox and stress response pathways.
    4. Decrease by causing unregulated motility, which has significant energy costs.

8. Paper Information and Licensing

8.1. Snippet paper

  • Peifer M. 2021. Looking back on a life of unacknowledged privilege and a call to action. Mol Biol Cell. 2021 32(11):1081-1085. doi: 10.1091/mbc.E21-01-0024.
  • This article is licensed for Creative Commons use using CC BY NC SA 3.0, which allows non-commercial re-use and adaptation with proper attribution and notation of any changes.

8.2. Main paper

  • Al-Shayeb B, Schoelmerich MC, West-Roberts J, Valentin-Alvarado LE, Sachdeva R, Mullen S, Crits-Christoph A, Wilkins MJ, Williams KH, Doudna JA, Banfield JF. 2022. Borgs are giant genetic elements with potential to expand metabolic capacity. Nature. 610(7933):731-736. doi: 10.1038/s41586-022-05256-1
  • 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.

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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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