Insight into the symbiotic lifestyle of DPANN archaea revealed by agriculture and genome analyzes


DPANN superphylum is a group of symbiotic microorganisms classified based on their genetic contents and some examples of cultivation experiments. Although the genome information of DPANN archaea is increasing year by year, most of it has remained uncultivated, limiting our knowledge of these organisms. Here, archaeon symbiotic acid-thermal (ARM-1) was successfully grown and characterized from the DPANN superphylum. We have determined its physiological, morphological and genomic characteristics in detail and obtained experimental evidence of a symbiotic lifestyle for this effect. Notably, ARM-1 is a symbiotic primitive strain that has demonstrated dependence on a range of host species in laboratory culture. The results contribute significantly to a true understanding of the physiology and ecology of DPANN archaea.


Decades of culture-independent analyzes have yielded proposals for several temporal primitive phyla with no cultivable representative. Members of the DPANN (abbreviation for the names of the first phyla comprising phyla Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanohaloarchaeota, and Nanoarchaeota), an archaeal group consisting of at least 10 of these temporary phyla, are generally considered obligate symbionts dependent on other microorganisms. While many drafts/whole-genome sequences of DPANN thrushes are available and their biological functions have been largely predicted, only a few examples of their successful in vitro cultivation have been reported, limiting our knowledge of their symbiotic lifestyles. Here, we investigated the physiology, morphology, and host specificity of an implication of phylum”Candidatus Microarchaeota” (ARM-1) which belongs to the DPANN superprotective by cultivation. We constructed a stable plant culture system consisting of ARM-1 and its parent host metallosphyra s. AS-7 belong to the command Solvoloples. Additional host switching experiments confirmed that ARM-1 grew on five different primitive species of three genera—metallosphyraAnd asdianos, And sacralopsIt arises from hot and acidic environments that are geologically distinct. The results indicated that there are DPANN archaea that can grow depending on a variety of hosts. Genomic analyzes demonstrated the inferred metabolic capabilities, common/unique genetic contents of ARM-1 among representatives of the cultured microbes, and the potential for horizontal gene transfer between ARM-1 and members of the system. Solvoloples. Our report sheds light on the symbiotic lifestyles of DPANN archaea and will contribute to elucidating their biological/environmental functions.


    • accepted November 12, 2021.
  • Author contributions: Research designed for HDS, AS, and NK; HDS, NN, AS, and NK conducted research; NN and NK did field sampling; HDS, MY and MS contributed new analytical reagents/tools; HDS, SK, TI and MO data analyzed; HDS and NK wrote the paper.

  • The book declares no competing interest.

  • This article is a direct PNAS submission.

  • This article contains supporting information online at

data availability

16S rRNA gene sequence data supporting the results of this study have been deposited in GenBank under accession number. LC490573 – LC490578. The genomic sequences of ARM-1 and metallosphyra s. AS-7 has been deposited with raw read data under the following accession numbers: AP024486 (ARM-1 genome), AP024487 (AS-7 genome), DRR248897 (PacBio RS II long reads), and DRR248898 (Illumina MiSeq short reads). All study data are included in the article and/or supporting information.

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