Genomic insights into the Archaea inhabiting an Australian radioactive legacy site

Abstract

18During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at 19 the Little Forest Legacy Site (LFLS, Sydney, Australia). The microbial function and population 20 dynamics during a rainfall event using shotgun metagenomics has been previously investigated. This 21 revealed a broad abundance of candidate and potentially undescribed taxa in this iron-rich, 22 radionuclide-contaminated environment. 23Here, applying genome-based metagenomic methods, we recovered 37 refined archaeal bins (≥50% 24 completeness, ≤ 10% redundancy) from 10 different major lineages. They were, for the most part, 25 included in 4 proposed lineages within the DPANN supergroup (LFWA-I to IV) and 26 Methanoperedenaceae. 27The new Methanoperedens spp. bins, together with previously published data, suggests a potentially 28 widespread ability to use nitrate (or nitrite) and metal ions as electron acceptors during the anaerobic 29 oxidation of methane by Methanoperedens spp. 30 While most of the new DPANN lineages show reduced genomes with limited central metabolism 31 typical of other DPANN, the candidate species from the proposed LFWA-III lineage show some 32 unusual features not often present in DPANN genomes, i.e. a more comprehensive central metabolism 33 and anabolic capabilities. While there is still some uncertainty about the capabilities of LFW-121_3 34 and closely related archaea for the biosynthesis of nucleotides de novo and amino acids, it is to date 35 the most promising candidate to be a bona fide free-living DPANN archaeon. 36 environments such as rice fields and ocean floors before it is released into the atmosphere [12]. Our 64 previous research showed that the archaeal community in the LFLS trenches was mainly composed of 65 methanogens and anaerobic methane oxidisers (ANME-2d) from the Methanomicrobia class and 66 DPANN archaea [3]. While they constituted a minor component of the community, they still may 67 have an important role in facilitating redox cycling and therefore impacting upon contaminant 68 mobilisation. 69 Here we describe the analysis of 37 new archaeal genomes with different degrees of completeness, 70 derived from samples collected in a legacy radioactive waste trench at the LFLS during a redox 71 cycling event. We present evidence of four new DPANN lineages and six non-conspecific 72 Methanoperedens sp. genomes, while exploring their potential role in the biogeochemical cycles and 73 uniqueness. 74 Material and Methods 75 Data source and experimental details 76 Raw sequencing reads from ENA project PRJEB14718 [3] were reanalysed, this time using 77 genome-based metagenomic methodologies in order to better understand the contributions of the 78 Archaea in the LFLS groundwater to the biogeochemistry of the site. Briefly, samples were collected 79 in triplicate over a period of 47 days at 4 time-points (0, 4, 21 and 47 days) after an intense rainfall 80 event that completely filled the trench. Thorough chemical and radiochemical analyses were 81 conducted on the samples in...

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' .…”

Indirect Routes to Aminoacyl-tRNA: The Diversity of Prokaryotic Cysteine Encoding Systems

“…Another SepRS-like homolog was found in a metagenomic bin of a Micrarchaeota Alv-FOS5-group ( Moussard et al, 2006 ) archaeon whose sequence was assembled from Guaymas Basin hydrothermal vent metagenomes ( Figure 4A and Figure 8 ). No other example was found in the public genome/metagenome sequence repositories we examined, probably due to the limited distribution of this archaeal group within populations of particular hydrothermal vents ( Moussard et al, 2006 ; Dombrowski et al, 2018 ; Vázquez-Campos et al, 2021 ). The sequence of the Alv-FOS5-group homolog is highly degenerated with multiple mutations and small insertions and deletions ( Figure 8 ).…”

Metagenomic discovery ofCandidatusParvarchaeales related lineages sheds light on the adaptation and diversification from neutral-thermal to acidic-mesothermal environments

“…The presence of 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, another ARMAN archaea - Micrarchaeota have been 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 non-extreme habitats like underground water (He et al 2021; Sakai et al 2022; Vázquez-Campos et al 2021). In contrast, Parvarchaeota appear to inhabit a narrower range of habitats.…”