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Introduction: Host-microbe interactions are pivotal in host biology, ecology, and evolution. Recent developments in sequencing technologies have provided newer insights into the same through the hologenome concept. Methods: We report here the study on metagenome-assembled genomes (MAGs) associated with Candida tropicalis (studied through shotgun metagenome sequencing), adding to the knowledge about endomicrobiomes of yeast. De novo assembly and binning recovered two partial archaeal genomes, taxonomically belonging to the phylum Asgardarchaeota. Results and Discussion: The phylogenomic analysis based on the core genes revealed that both the binned genomes cladded separately with the less studied and uncultivated 'Candidatus' superphylum, designated as Asgard archaea (the nearest known relative of eukaryotes). Between the two binned genomes, the average nucleotide index (ANI) was 71.2%. The average nucleotide identities (ANI) of the two binned genomes with 'Candidatus Heimdallarchaeota' were 60.4-61.2%. The metabolic pathways of both the binned genomes predicted genes belonging to sulfur reduction, Kreb's pathway, glycolysis, and C1 carbon metabolism. Further, both the binned genomes were predicted to support autotrophic as well as the heterotrophic mode of growth, which might probably help the host in its nutritional requirements also. Further, the genomes showed few eukaryotic signature proteins (ESPs) and SNARE proteins indicating that members of Asgardarchaeota are the closest relatives of eukaryotes. The gaps present in the metabolic potential of the MAGs obtained and the absence of a few essential pathways shows that they are probably in a symbiotic relationship with the host. The present study, reports for the first-time endosymbiosis of Asgard archaea with yeast. It also provides insights into the metabolic potential, ecology, evolutionary history, and endosymbiotic nature of the important but 160 poorly studied Asgard archaea. [ABSTRACT FROM AUTHOR]

Asgard archaea, believed to be the ancestor of eukaryotes, constitute a new superphylum prevalent in diverse sediment environments. Their distribution and metabolic potentials are diversified and elusive. In the present study, the distribution and genomic characteristics of Asgard archaea in the Haima cold seep of the South China Sea (SCS) were investigated. In total, we obtained 48 high-quality metagenome-assembled genomes (MAGs), which fell into 7 separated lineages affiliated with the phyla Lokiarchaeota, Thorarchaeota, Heimdallarchaeota and Gerdarchaeota. These Asgard archaea were mainly distributed in the cold seep but rarely detected in the control marine sediments. We found that Asgard might encode complex CRISPR-Cas systems, which likely protected the archaea against abundant viruses in cold seep sediments. Phylogenomic tree indicated the novelty of cold-seep Asgard archaea, and highlighted that MAG HM7_B34 was affiliated with the newly proposed Gerdarchaeota phylum. Metabolic reconstruction indicated that Gerdarchaeota in the Haima cold seep were obligate anaerobic archaea and might undergo autotrophic lifestyle using the Wood-Ljungdahl pathway. Moreover, Gerdarchaeota might metabolize formaldehyde and likely had the ability to hydrolyze oligosaccharides including chitin. Altogether, our study expands the cognition of Asgard archaea in terms of spatial distribution, biodiversity and carbon cycle in cold seep ecosystems. • The present study provides an unprecedented opportunity to retrieve metagenome-assembled genomes (MAGs) of novel Asgard. • The taxonomic diversity, spatial distribution and metabolic potentials of Asgard archaea were illustrated. • Anaerobic Gerdarchaeota was highlighted for their carbon assimilation, chitin degradation and CRISPR-Cas system. • This work casts lights into the characteristics of the Asgard archaea inhabiting cold seep ecosystems. [ABSTRACT FROM AUTHOR]

Increasing number of metagenome sequencing studies have proposed a central metabolic role of still understudied Archaeal members in natural and artificial ecosystems. However, their role in hydrocarbon cycling, particularly in the anaerobic biodegradation of aliphatic and aromatic hydrocarbons, is still mostly unknown in both marine and terrestrial environments. In this work, we focused our study on the metagenomic characterization of the archaeal community inhabiting the Mar Piccolo (Taranto, Italy, central Mediterranean) sediments heavily contaminated by petroleum hydrocarbons and polychlorinated biphenyls (PCB). Among metagenomic bins reconstructed from Mar Piccolo microbial community, we have identified members of the Asgardarchaeota superphylum that has been recently proposed to play a central role in hydrocarbon cycling in natural ecosystems under anoxic conditions. In particular, we found members affiliated with Thorarchaeota, Heimdallarchaeota, and Lokiarchaeota phyla and analyzed their genomic potential involved in central metabolism and hydrocarbon biodegradation. Metabolic prediction based on metagenomic analysis identified the malonyl-CoA and benzoyl-CoA routes as the pathways involved in aliphatic and aromatic biodegradation in these Asgardarchaeota members. This is the first study to give insight into the archaeal community functionality and connection to hydrocarbon degradation in marine sediment historically contaminated by hydrocarbons. [ABSTRACT FROM AUTHOR]