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 in a waste trench during a rainfall event have been previously investigated revealing a broad abundance of candidate and potentially undescribed taxa in this iron-rich, radionuclide-contaminated environment. Applying genome-based metagenomic methods, we recovered 37 refined archaeal MAGs, mainly from undescribed DPANN Archaea lineages without standing in nomenclature and ‘Candidatus Methanoperedenaceae’ (ANME-2D). Within the undescribed DPANN, the newly proposed orders ‘Ca. Gugararchaeales’, ‘Ca. Burarchaeales’ and ‘Ca. Anstonellales’, constitute distinct lineages with a more comprehensive central metabolism and anabolic capabilities within the ‘Ca. Micrarchaeota’ phylum compared to most other DPANN. The analysis of new and extant ‘Ca. Methanoperedens spp.’ MAGs suggests metal ions as the ancestral electron acceptors during the anaerobic oxidation of methane while the respiration of nitrate/nitrite via molybdopterin oxidoreductases would have been a secondary acquisition. The presence of genes for the biosynthesis of polyhydroxyalkanoates in most ‘Ca. Methanoperedens’ also appears to be a widespread characteristic of the genus for carbon accumulation. This work expands our knowledge about the roles of the Archaea at the LFLS, especially, DPANN Archaea and ‘Ca. Methanoperedens’, while exploring their diversity, uniqueness, potential role in elemental cycling, and evolutionary history.

Nanobdella aerobiophila gen. nov., sp. nov., a thermoacidophilic, obligate ectosymbiotic archaeon, and proposal of Nanobdellaceae fam. nov., Nanobdellales ord. nov. and Nanobdellia class. nov.

“…Pacearchaeales, and Ca . Parvarchaeales were included in a class- or phylum-level clade (c__Nanoarchaeia or p__Nanoarchaeota, respectively, in GTDB), as previously reported [57]. This phylum-level clade could be distinguished from other phylum-level clades, such as ‘ Nanohaloarchaeota ’ and ‘ Microcaldota ’.…”

Metagenomic Discovery of “ Candidatus Parvarchaeales”-Related Lineages Sheds Light on Adaptation and Diversification from Neutral-Thermal to Acidic-Mesothermal Environments

“…The presence of the ETC and the TCA cycle in oxygen-limited environments is possibly associated with the consumption of oxygen rather than aerobic respiration. Although initially discovered in AMD, other ARMAN archaea, Micrarchaeota, have tremendously expanded in phylogenetic diversity and have been found to exist in a variety of environments, including extreme habitats such as hot springs and radioactive sites as well as nonextreme habitats like underground water ( 17 – 19 ). In contrast, Parvarchaeota appear to inhabit a narrower range of habitats.…”