During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in three-metre-deep, unlined trenches. Prior research has investigated functional and population dynamics during a rainfall event using shotgun metagenomics. This revealed a broad abundance of candidate and potentially undescribed taxa in this iron-rich, radionuclide-contaminated environment. Thus, we explored the same dataset through genomic reconstruction and phylogenomics but focusing specifically in Archaea.
In total, we recovered 318 refined bins with ≥50% completeness and ≤10% redundancy, 37 of which belonged to Archaea. A concatenated protein tree was constructed using 44 highly conserved universal or Archaea-specific ribosomal proteins extracted from the archaeal MAGs plus > 200 non-redundant diverse genomes from public databases. Phylogenomic analysis revealed archaeal bins corresponded to 10 different phyla, including 4 newly proposed lineages within the DPANN supergroup (LFWA-I to IV, 15 bins), Methanosaetaceae (3), Methanoperedenaceae (6), Thermoplasmata (1), Micrarchaeota s. stricto (1), Diapherotrites (2), Woesearchaeota (1), Pacearchaeota (6), Altiarchaeota (1) and Thaumarchaeota (1).
While most of the new DPANN lineages show reduced genomes with limited central metabolism similar to other typical DPANN, the candidate species from the proposed LFWA-III lineage show some unusual features.
- First, they have complete de novo nucleotide biosynthesis pathways.
- Second, they harbour all genes needed for the biosynthesis of both thiamine and riboflavin.
- Third, they present a partial TCA cycle.
- And most importantly, fourth, they contain highly connected amino acid pathways that can be tracked all the way to carbon source assimilation.
These features may suggest a lesser dependence on a host or symbiotic partner. In addition, LFWA-III seems to be a diverse in the sampled trench with 11 MAGs suggested to belong to 10 different genera in a single family based on ANI/AAI relatedness.
Future research will attempt to discover the possible symbionts of the diverse DPANN organisms present in the site.