Genomic insights into the Archaea inhabiting an Australian radioactive legacy site

Abstract

During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (LFLS, Sydney, Australia). The microbial function and population dynamics during a rainfall event using shotgun metagenomics has been previously investigated. This revealed a broad abundance of candidate and potentially undescribed taxa in this iron-rich, radionuclide-contaminated environment.

Here, applying genome-based metagenomic methods, we recovered 37 refined archaeal bins (≥50% completeness, ≤10% redundancy) from 10 different major lineages. They were mostly included in 4 proposed lineages within the DPANN supergroup (LFWA-I to IV) and Methanoperedenaceae.

The new Methanoperedens spp. bins, together with previously published data, suggests a potentially widespread ability to use nitrate (or nitrite) and metal ions as electron acceptors during the anaerobic oxidation of methane by Methanoperedens spp.

While most of the new DPANN lineages show reduced genomes with limited central metabolism typical of other DPANN, the candidate species from the proposed LFWA-III lineage show some unusual features not often present in DPANN genomes, i.e. a more comprehensive central metabolism and anabolic capabilities.While there is still some uncertainty about the capabilities of LFW-121_3 and closely related archaea for the biosynthesis of nucleotides de novo, and amino acids, it is to date the most promising candidate to be the first bona fide free-living DPANN archaeon.

Repository Contents

genomes.tar: includes each of the reference and novel assembled MAG/bins used for analysis in the main manuscript as .tar.gz compressed folders. Each genome folder contains the output from:

Anvi'o,

EggNOG analysis with arNOG library,

InterProScan analysis,

rRNA search with Barrnap,

output from searching high heme cytochromes (≥10 heme binding sites in a single protein),

CAZy search output,

MEROPS output (BLASTp),

PSORTb, and

TCDB.

In the case of the new MAGs (i.e. LFW_Bin_00*, referred in the paper as LFW-*), some additional contents are included:

tRNAs from tRNAscan-SE, and

Prokka annotation files.

pangenomics.tar: includes the Anvi'o files for the pangenomic analysis of:

anme-2d.tar.gz: pangenome of Methanoperedens spp. based on 4 reference and 6 novel MAGs clustered with an MCL inflation value of 6.0. It also includes the output of ANI analysis (via pyANI) and AAI (via CompareM).

LFWA-III.tar.gz: pangenome analysis of the LFWA-III lineage ('Gugararchaeaceae) based on 2 reference and 8 novel MAGs clustered at inflation values of 1.0, 1.5 and 2.0. It also includes the output of ANI analysis (via pyANI) and AAI (via CompareM).

phylogeny.tar: includes the files required for the phylogenomic/phylogenetic analyses shown in the paper and the Supplementary Information:

rp44.tar.gz: phylogenomic analysis based on 44 universal and archaeal-specific ribosomal proteins (Figure 1 in paper). It also includes annotation files for iTOL.

NarG.tar.gz: phylogeny of NarG and relate molybdopterin oxidoreductase proteins (Figure 5 in paper).

LysJ-ArgD.tar.gz: phylogeny of LysJ/ArgD proteins and their orthologous (Figure S3 in paper).