Cave expedition

Learning objectives

  • Explore binning results from biofilm metagenomes in a greenhouse gas-emitting cave.
  • Seek evidence identifying the primary consumers (CO2 & CH4) within this extreme environment.

Cave Microbiome Sampling (a) General overview of the cave. The dashed line in panel a marks the stable gaseous chemocline between the volcanic gases (below the chemocline) and atmospheric air (above the chemocline). (b) Detailed images of the cave biofilms. (c) A closer look on the biofilm where mark 7 shows the bare cave wall after biofilm sampling.

Watch the "Sulfur Cave" video to see bubbles drifting along the invisible stream of greenhouse gases (for fun).

Precomputed data is stored in the /data/precomputed/cave_data folder, which contains the following: 1) Co-assembly of three samples (two from biofilm and one from the laboratory), 2) Depth table and 3) Binning results

Exercise

  • Analyze the microbial bins to identify which organism is utilizing CH₄ (methane) for growth. What is the taxonomic classification of this organism? Investigate the presence of relevant gene clusters responsible for methane metabolism.
  • Investigate whether it is common for organisms within the identified taxon to utilize CH₄ for growth. If not, outline the steps and analyses you would perform to confirm and demonstrate this metabolic capability.
  • Perform a similar investigation to identify which organism is fixing CO₂ for growth. What is the taxonomy of this organism, and what genes are involved in CO₂ fixation?
Tip 1: general directions
  • Assess bin quality using CheckM to evaluate completeness and contamination levels.
  • Assign taxonomies to the bins with GTDB-Tk for precise classification.
  • Predict open reading frames (ORFs) using Prodigal and functionally annotate the bins through EggNOG for a deeper understanding of their metabolic capabilities.
Tip 2
  • Investigate the gene annotation for methane monooxygenase and reductive TCA cycle and analyze the surrounding genomic regions to identify nearby genes and their associated protein functions.
  • Calculate the abundance of each bin by integrating the depth table with the binning results (use python/R).