Highly diverse Asgard archaea participate in organic matter degradation in coastal sediments

Abstract

<jats:title>ABSTRACT</jats:title><jats:p>Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes (MAGs) from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named as the “Gerdarchaeota”. Genomic analyses predict that Gerdarchaeota are facultative anaerobes in utilizing both organic and inorganic carbon. Unlike their closest relatives Heimdallarchaeota, Gerdarchaeota have genes encoding for cellulase and enzymes involving in the tetrahydromethanopterin-based Wood–Ljungdahl pathway. Transcriptomic evidence showed that all known Asgard archaea are capable of degrading organic matter, including peptides, amino acids and fatty acids, in different ecological niches in sediments. Overall, this study broadens the diversity of the mysterious Asgard archaea and provides evidence for their ecological roles in coastal sediments.</jats:p>

The Distribution of Bathyarchaeota in Surface Sediments of the Pearl River Estuary Along Salinity Gradient

“…We observed that the class Nitrosopumilales (MG-I) dominated in Thaumarchaeota (Supplementary Figure S3C), which was consistent with previous surveys (Liu et al, 2014;Xie et al, 2014). Loki-3, as the most abundant subgroup of Lokiarchaeota, usually inhabits the estuarine and marine sediments (Cai et al, 2019), which is consistent with the data on the PRE surface sediments presented herein (Supplementary Figure S3D). Thermoprofundales have been previously categorized into 16 subgroups, of which MBGD-8a and -8c are enriched in saline marine sediments; MBGD-9a and -9c are mostly found in non-saline environments, such as the freshwater, soil, and lake sediments; while MBGD-11 and -12 show no preference in terms of salinity, and are found in a variety of habitats (Zhou et al, 2019).…”

“…Taxonomic assignment of the representative archaeal sequences was achieved using the SILVA database (release 132) (Quast et al, 2012). The sequences of Bathyarchaeota (Zhou et al, 2018a), Thermoprofundales [Marine Benthic Group D (MBG-D)] (Zhou et al, 2019), and Lokiarchaeota (Cai et al, 2019)…”

Design of targeted primers based on 16S rRNA sequences in meta-transcriptomic datasets and identification of a novel taxonomic group in the Asgard archaea

“…With the application of single cell genome and metagenome sequencing and assembly, the number of phyla in Archaea domain has increased to more than twenty, and these phyla clustered to Euryarchaota and three superphyla-TACK, DPANN, and Asgard [15]. According to the assembled genomes from metagenome sequencing, the Asgard superphylum embraced six phyla: Lokiarchaeota, Thorarchaeota, Heimdallarchaeota, Odinarchaeota, Helarchaeota, and Gerdarchaeota [16][17][18][19]. The phylogenetic and comparative genomic analysis showed that Asgard archaea share a common ancestry with eukaryotes and even putatively have eukaryotic signatures [17], initiating a discussion about three or two domains [20][21][22][23][24].…”