Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota

Abstract

Small acidophilic archaea belonging to Micrarchaeota and Parvarchaeota phyla are known to physically interact with some Thermoplasmatales members in nature. However, due to a lack of cultivation and limited genomes on hand, their biodiversity, metabolisms, and physiologies remain largely unresolved. Here, we obtained 39 genomes from acid mine drainage (AMD) and hot spring environments around the world. 16S rRNA gene based analyses revealed that Parvarchaeota were only detected in AMD and hot spring habitats, while Micrarchaeota were also detected in others including soil, peat, hypersaline mat, and freshwater, suggesting a considerable higher diversity and broader than expected habitat distribution for this phylum. Despite their small genomes (0.64-1.08 Mb), these archaea may contribute to carbon and nitrogen cycling by degrading multiple saccharides and proteins, and produce ATP via aerobic respiration and fermentation. Additionally, we identified several syntenic genes with homology to those involved in iron oxidation in six Parvarchaeota genomes, suggesting their potential role in iron cycling. However, both phyla lack biosynthetic pathways for amino acids and nucleotides, suggesting that they likely scavenge these biomolecules from the environment and/or other community members. Moreover, low-oxygen enrichments in laboratory confirmed our speculation that both phyla are microaerobic/anaerobic, based on several specific genes identified in them. Furthermore, phylogenetic analyses provide insights into the close evolutionary history of energy related functionalities between both phyla with Thermoplasmatales. These results expand our understanding of these elusive archaea by revealing their involvement in carbon, nitrogen, and iron cycling, and suggest their potential interactions with Thermoplasmatales on genomic scale.

Fig. 1. Phylogenetic analyses of Micrarchaeota and Parvarchaeota genomes

The phylogenetic tree was constructed based on 16 concatenated ribosomal protein sequences from each Micrarchaeota and Parvarchaeota genome and reference archaeal genomes (or scaffolds with the target ribosomal protein sequences) (Materials and methods). The three archaeal superphyla TACK, Asgard and DPANN, and the number of genomes included for each phylum are shown. Previously published genomes are indicated by arrows, and the metagenomic datasets of “YNP hot spring” and “FK AMD outflow (2010)” were retrieved from public databases. Bootstrap values are based on 100 replicates

Fig. 2

Comparative analyses of gene contents of Micrarchaeota and Parvarchaeota genomes. For a Micrarchaeota and b Parvarchaeota, the phylogeny cluster pattern (from Fig. 1) and the corresponding KEGG Orthology clustering pattern (based on occurrence of KOs in each genome; see Materials and methods) were compared, and the genomes were manually assigned to several clades/groups based on the cluster patterns. The same clade/group in a phylogeny cluster and gene contents clusters were linked with a solid line

Fig. 3

Overview of potential metabolic capabilities. Metabolic pathways were constructed based on the annotation of predicted genes (Materials and methods) and shown for a Micrarchaeota and b Parvarchaeota taxa. The glycolysis and gluconeogenesis pathways, the pentose phosphate pathway, the pyruvate metabolism, beta-oxidation of fatty acids, the TCA cycle and oxidative phosphorylation chain, protein biosynthesis-related pathways, membrane transporters, and other significant metabolisms are shown. The corresponding enzymes are represented by an ID in the figure and Supplementary Table 8 contains the gene copy number of each enzyme as well as of transporters, carbohydrate-degrading enzymes and peptidases. G6P glucose 6-phosphate, F6P fructose 6-phosphate, F1,6BP fructose 1,6-bisphosphate, GAP glyceraldehyde-3-phosphate, 3PG 3-phosphoglycerate, 2PG 2-phosphoglycerate, PEP phosphoenolpyruvate, KDG 2-keto-3-deoxygluconate, GA glyceraldehyde, G3P glycerol-3-phosphate, DHAP dihydroxyacetone phosphate, Ribu-5P ribulose 5-phosphate, Xylu-5P xylulose 5-phosphate, Ribo-5P ribose-5-phosphate, PRPP phosphoribosyl pyrophosphate, Oaa oxaloacetate, Cit citrate, Iso isocitrate, 2-Oxo 2-oxoglutarate, Suc-CoA succinyl-CoA, Succ succinate, Fum fumarate, Mal malate, Glu glutamate, Gln Glutamine, Fd ferredoxin, 3-HB-CoA 3-hydroxybutyryl-CoA, But-CoA Butyryl-CoA, As arsenic

Fig. 4

Cluster of rusticyanin related genes detected in Parvarchaeota. a A rusticyanin cluster was detected in 6 Parvarchaeota genomes between a MscS (small-conductance mechanosensitive channel-like) gene and a hypothetical protein and a PEP (phosphoenolpyruvate) carboxykinase gene (middle panel). No inserted cluster was found in other Parvarchaeota (above panel). The cluster includes two rusticyanin proteins, one multicopper protein and three hypothetical proteins (bottom panel). The amino acid length of all proteins are shown. b Phylogeny analyses of rusticyanin protein sequences encoded in ARMAN (those two in the cluster and others detected in ARMAN) and genomes of confirmed iron oxidizers, also including the similar key iron oxidase of sulfocyanin. The tree was built using MEGAN (version 7.0.14) using Maximum Likelihood method with 100 replicates, bootstrap numbers are shown

Fig. 5

Laboratory enrichment of ARMAN from a simulated AMD system. a Diagram showing the experimental design of the enrichment experiment (Materials and methods). The dissolved oxygen concentration was determined when collecting enriched cells. b Relative abundance of taxa in the inoculum and enrichments with different nutriments. The exact numbers for ARMAN taxa are shown, and those from MDA metagenomes are indicated by asterisks. c Circos-based alignment of genomes from enriched communities against those from environmental samples reported in this study. The alignment of Micrarchaeota sp. 2 contained too many scaffolds and is not shown. Each scale on the scaffold represents a length of 20 kbp

Fig. 6

Phylogenetic analyses of Thermoplasmatales related taxa detected in the microbial communities analyzed in this study. The tree was built using all available Thermoplasmatales related rpS3 sequences detected in the metagenomes, and those of related published genomes (in italic bold) and included A-plasma, I-plasma, E-plasma, G-plasma (also Cuniculiplasma spp.; four genomes in total, while C_DKE lacks rpS3 due to low completeness), Thermoplasma volcanium, Thermoplasma acidophilum, Thermogymnomonas acidicola, and Thermoplasmatales archaeon B_DKE. For a comparison, the G-plasma related spp. in the analyzed communities sharing 100% rpS3 sequence similarity with published genomes, were binned to obtain their genomes (indicated by stars), and these eight G-plasma related genomes share high 16S rRNA simiarity (98.5–100%) and ANI (94.1–99.4%)