Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota

Chen, Lin-Xing; Mendez-Garcia, Celia; Dombrowski, Nina; Servin-Garciduenas, Luis E.; Eloe-Fadrosh, Emiley A.; Fang, Bao-Zhu; Luo, Zhen-Hao; Tan, Sha; Zhi, Xiao-Yang; Hua, Zheng-Shuang; Martinez-Romero, Esperanza; Woyke, Tanja; Huang, Li-Nan; Sanchez, Jesus; Pelaez, Ana Isabel; Ferrer, Manuel; Baker, Brett J.; Shu, Wen-Sheng

doi:10.1038/s41396-017-0002-z

Title: Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota

Journal Article · Fri Dec 08 00:00:00 EST 2017 · The ISME Journal

DOI:https://doi.org/10.1038/s41396-017-0002-z· OSTI ID:1434028

^[1];

^[2];

^[3]; Servin-Garciduenas, Luis E. ^[4]; Eloe-Fadrosh, Emiley A. ^[5]; Fang, Bao-Zhu ^[1]; Luo, Zhen-Hao ^[1]; Tan, Sha ^[1]; Zhi, Xiao-Yang ^[6]; Hua, Zheng-Shuang ^[1]; Martinez-Romero, Esperanza ^[7]; Woyke, Tanja ^[5]; Huang, Li-Nan ^[1]; Sanchez, Jesus ^[8]; Pelaez, Ana Isabel ^[8]; Ferrer, Manuel ^[9]; Baker, Brett J. ^[3]; Shu, Wen-Sheng ^[10]

Sun Yat-Sen Univ., Guangzhou, (China). State Key Lab. of Biocontrol, Guangdong Key Lab. of Plant Resources and College of Ecology and Evolution
Univ. of Oviedo (Spain). Dept. of Functional Biology and Univ. Inst. of Biotechnology of Asturias (IUBA); Univ. of Illinois, Urbana, IL (United States). Carl R. Woese Inst. for Genomic Biology
Univ. of Texas, Austin, TX (United States). Dept. of Marine Science and Marine Science Inst.
National Autonomous Univ. of Mexico, Morelia (Mexico). Lab. of Microbiomics and National School of Higher Studies Morelia
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Yunnan Univ., Kunming (China). Yunnan Inst. of Microbiology
National Autonomous Univ. of Mexico, Morelia (Mexico). Dept. of Ecological Genomics and Center for Genomic Sciences
Univ. of Oviedo (Spain). Dept. of Functional Biology and Univ. Inst. of Biotechnology of Asturias (IUBA)
Spanish National Research Council (CSIC), Madrid (Spain). Inst. of Catalysis
South China Normal Univ., Guangzhou (China). School of Life Sciences

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. For this study, 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 Parvarchae ota 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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); Univ. of California, Berkeley, CA (United States); National Center for Biotechnology Information (NCBI); China Univ. of Geosciences, Wuhan (China); Univ. of Massachusetts, Amherst, MA (United States); Univ. of Konstanz (Germany); National Natural Science Foundation of China (NSFC); Alfred P. Sloan Foundation; National Autonomous Univ. of Mexico, Morelia (Mexico)

Grant/Contract Number:: AC02-05CH11231; 31600101; U1201233; 31570500; PAPIIT IA210617

OSTI ID:: 1434028

Journal Information:: The ISME Journal, Vol. 12, Issue 3; Related Information: © 2017 The Author(s) 2017, under exclusive licence to Macmillan Publishers Limited, part of Springer Nature.; ISSN 1751-7362

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 56 works

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