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Metabolic Versatility of Small Archaea Micrarchaeota and Parvarchaeota Lawrence Berkeley National Laboratory Recent Work Title Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota. Permalink https://escholarship.org/uc/item/1vc6t690 Journal The ISME journal, 12(3) ISSN 1751-7362 Authors Chen, Lin-Xing Méndez-García, Celia Dombrowski, Nina et al. Publication Date 2018-03-01 DOI 10.1038/s41396-017-0002-z Peer reviewed eScholarship.org Powered by the California Digital Library University of California The ISME Journal (2018) 12:756–775 https://doi.org/10.1038/s41396-017-0002-z ARTICLE Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota 1 2,3 4 5 Lin-Xing Chen ● Celia Méndez-García ● Nina Dombrowski ● Luis E. Servín-Garcidueñas ● 6 1 1 1 7 1 Emiley A. Eloe-Fadrosh ● Bao-Zhu Fang ● Zhen-Hao Luo ● Sha Tan ● Xiao-Yang Zhi ● Zheng-Shuang Hua ● 8 6 1 2 2 Esperanza Martinez-Romero ● Tanja Woyke ● Li-Nan Huang ● Jesús Sánchez ● Ana Isabel Peláez ● 9 4 10 Manuel Ferrer ● Brett J. Baker ● Wen-Sheng Shu Received: 5 April 2017 / Revised: 26 August 2017 / Accepted: 9 October 2017 / Published online: 8 December 2017 © The Author(s) 2018. This article is published with open access 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 1234567890 world. 16S rRNA gene based analyses revealed that Electronic supplementary material The online version of this article Parvarchaeota were only detected in AMD and hot spring (https://doi.org/10.1038/s41396-017-0002-z) contains supplementary habitats, while Micrarchaeota were also detected in others material, which is available to authorized users. including soil, peat, hypersaline mat, and freshwater, * Brett J. Baker suggesting a considerable higher diversity and broader than [email protected] expected habitat distribution for this phylum. Despite their * Wen-Sheng Shu small genomes (0.64–1.08 Mb), these archaea may con- [email protected] tribute to carbon and nitrogen cycling by degrading multiple saccharides and proteins, and produce ATP via aerobic 1 State Key Laboratory of Biocontrol, Guangdong Key Laboratory respiration and fermentation. Additionally, we identified of Plant Resources, College of Ecology and Evolution, Sun Yat- Sen University, Guangzhou 510275, People’s Republic of China several syntenic genes with homology to those involved in iron oxidation in six Parvarchaeota genomes, suggesting 2 Departamento de Biología Funcional-IUBA, Universidad de Oviedo, Oviedo, Spain their potential role in iron cycling. However, both phyla lack biosynthetic pathways for amino acids and nucleotides, 3 Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, USA suggesting that they likely scavenge these biomolecules 4 from the environment and/or other community members. Department of Marine Science, University of Texas Austin, fi Marine Science Institute, Port Aransas, TX 78373, USA Moreover, low-oxygen enrichments in laboratory con rmed 5 our speculation that both phyla are microaerobic/anaerobic, Laboratory of Microbiomics, National School of Higher Studies fi fi Morelia, National University of Mexico, Morelia, Michoacan based on several speci c genes identi ed in them. 58190, Mexico Furthermore, phylogenetic analyses provide insights into 6 Department of Energy Joint Genome Institute, Walnut Creek, CA the close evolutionary history of energy related functional- 94598, USA ities between both phyla with Thermoplasmatales. These 7 Yunnan Institute of Microbiology, Yunnan University, results expand our understanding of these elusive archaea Kunming 650091, People’s Republic of China by revealing their involvement in carbon, nitrogen, and iron 8 Department of Ecological Genomics, Center for Genomic cycling, and suggest their potential interactions with Sciences, National University of Mexico, Cuernavaca, Thermoplasmatales on genomic scale. Morelos 62210, Mexico 9 Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain 10 School of Life Sciences, South China Normal University, Guangzhou 510631, People’s Republic of China Metabolic versatility of ARMAN 757 Introduction anaerobic, thus enrichments with inoculum from AMD systems were performed for these elusive archaea (Sup- Archaea constitute a considerable portion of microbial plementary Fig. 1). diversity, and play significant roles in many biogeochemical cycles on Earth [1]. However, compared to bacteria they are much less understood and fewer genomes have been Materials and methods sequenced [2]. The recently delineated superphylum DPANN includes several phyla of archaea with small cell ARMAN genomes and related metagenomes in and genome sizes and limited metabolic capabilities [3–6]. public database To date, 48 DPANN draft genomes are available (Supple- mentary Table 1; see references therein) and only two In NCBI database, there are two Micrarchaeota and two symbiotic Nanoarchaeota co-cultures have been obtained Parvarchaeota genomes reported from Iron Mountain: [5, 7]. ARMAN-1 (NCBI accession number, PRJNA349044), Two DPANN phyla, Micrarchaeota and Parvarchaeota, ARMAN-2 (PRJNA38565), ARMAN-4 (PRJNA38567), referred to as Archaeal Richmond Mine Acidophilic and ARMAN-5 (PRJNA38569), which were included for Nanoorganisms (ARMAN), were first reported in acid analyses in this study. mine drainage (AMD) biofilms of Iron mountain (Rich- A metagenomic data set sampled from the Fankou mine mond, CA, USA) and are among the smallest micro- tailings AMD outflow in 2010 (sample abbreviation: organisms described to date [8, 9]. The AMD biofilms in FK_AMD_2010), which was published previously [15], Iron Mountain have been comprehensively studied for was included in this study to retrieve ARMAN genomes microbial ecology and evolution [10]. Four genomes of from newly assembled contigs. The ultra-small cells were ARMAN have been obtained from this site, including collected by filtering the AMD outflow through 0.22 μm ARMAN-1 and ARMAN-2 from Micrarchaeota, and pore size filters, which were preserved for DNA extraction ARMAN-4 and ARMAN-5 from Parvarchaeota. The [15]. metabolic functions of ARMAN-2, -4 and -5 in the AMD The available ARMAN genomes were also used as biofilms have been speculated based on metaproteomic references to search for additional ARMAN sequences in analyses [11], while ARMAN-1 was published recently publicly available contigs/scaffolds of >3000 metagenomic only to report its CRISPR–Cas system [12]. Interestingly, data sets deposited in the IMG/M system (alignment ARMAN cells were observed having interactions with length ≥ 250 bp, similarity ≥ 75%). This analysis retrieved Thermoplasmatales cells via pili-like structures [11], and one additional metagenomic data set from Obsidian Pool in this phenomenon was further documented using cryo- the Yellowstone National Park (SRA accession, genic transmission electron microscope technology [13], SRP099390; IMG genome ID, 3300002966) with while the ecological significance of such interactions ARMAN-related genomic sequences (sample abbreviation: remains unclear. Moreover, ARMAN-specificPCRpri- YNP_OP). Obsidian Pool (N44.36°, W110.26°) was mers and metagenomics have revealed their occurrence in reported as a mesothermal hot spring (56 °C; Supplemen- many other AMD-related environments [14–17], indi- tary Table 2) [18]. cating wide distributions of related microorganisms in nature. Study sites, sampling, DNA extraction, and Despite these investigations described above, we know sequencing little about their biodiversity, environmental distribution (in other acidic and non-acidic environments), physiologies, Metagenomic data sets from two AMD and two hot spring and roles in biogeochemical cycling. To address these gaps, environments were collected and analyzed in this study we assembled and binned 39 new genomes from metage- (Supplementary Fig. 2 and Supplementary Table 2); the site nomic datasets obtained from two AMD and three hot descriptions and experimental procedures (e.g., sampling, spring related environments around the world, and the DNA extraction and sequencing) are detailed below. environmental distribution of Micrarchaeota and Parvarch- aeota taxa were evaluated by analyzing 16S rRNA gene (1) Fankou AMD outflow (FK_AMD_2014). Fankou sequences from those new genomes and NCBI and IMG/M mine is located in north Guangdong province of databases. Metabolic potentials of Micrarchaeota and Par- China (N25.05°, E113.67°), and the microbial ecol- varchaeota were predicted based on functional annotation of ogy of this site was deeply studied previously, to their genes, to reveal their metabolic functions and potential reveal the microbial diversity and composition at roles in nature. Additionally, genomic information likely spatial and temporal scales of the mine tailings [19], suggested that ARMAN spp. are microaerobic and/or the shifts of microbial composition and function 758 L-X Chen et al. across the tailings acidification processes [20], and sequenced on an Illumina HiSeq2000 platform with also the metatranscriptomic activities in the related a PE 100 bp kit. AMD systems [14, 15]. Microorganisms in AMD (4) Tengchong geothermal area (TC_Endo). The Teng- outflow were collected in September, 2014, using chong geothermal
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