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A New Candidate Phylum in the Archaea from High-Temperature Acidic Iron Mats in Yellowstone National Park

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A New Candidate Phylum in the Archaea from High-Temperature Acidic Iron Mats in Yellowstone National Park The ISME Journal (2013) 7, 622–634 & 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13 www.nature.com/ismej ORIGINAL ARTICLE Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park Mark A Kozubal1, Margaret Romine2, Ryan deM Jennings1, Zack J Jay1, Susannah G Tringe3, Doug B Rusch4, Jacob P Beam1, Lee Ann McCue2 and William P Inskeep1 1Department of Land Resources and Environmental Sciences and Thermal Biology Institute, Montana State University, Bozeman, MT, USA; 2Environmental Microbiology Group, Pacific Northwest National Laboratory, Richland, WA, USA; 3DOE Joint Genome Institute, Walnut Creek, CA, USA and 4Department of Biology, Indiana University, Bloomington, IN, USA Geothermal systems in Yellowstone National Park (YNP) provide an outstanding opportunity to understand the origin and evolution of metabolic processes necessary for life in extreme environments including low pH, high temperature, low oxygen and elevated concentrations of reduced iron. Previous phylogenetic studies of acidic ferric iron mats from YNP have revealed considerable diversity of uncultivated and undescribed archaea. The goal of this study was to obtain replicate de novo genome assemblies for a dominant archaeal population inhabiting acidic iron- oxide mats in YNP. Detailed analysis of conserved ribosomal and informational processing genes indicates that the replicate assemblies represent a new candidate phylum within the domain Archaea referred to here as ‘Geoarchaeota’ or ‘novel archaeal group 1 (NAG1)’. The NAG1 organisms contain pathways necessary for the catabolism of peptides and complex carbohydrates as well as a bacterial-like Form I carbon monoxide dehydrogenase complex likely used for energy conservation. Moreover, this novel population contains genes involved in the metabolism of oxygen including a Type A heme copper oxidase, a bd-type terminal oxidase and a putative oxygen-sensing protoglobin. NAG1 has a variety of unique bacterial-like cofactor biosynthesis and transport genes and a Type3-like CRISPR system. Discovery of NAG1 is critical to our understanding of microbial community structure and function in extant thermophilic iron-oxide mats of YNP, and will provide insight regarding the evolution of Archaea in early Earth environments that may have important analogs active in YNP today. The ISME Journal (2013) 7, 622–634; doi:10.1038/ismej.2012.132; published online 15 November 2012 Subject Category: microbial ecology and functional diversity of natural habitats Keywords: extremophiles; geothermal; Yellowstone National Park; heme copper oxidase; carbon monoxide; iron-oxides Introduction methanogens and halophiles together in the phylum Euryarchaeota, and a second major phylum (Cre- Although members of the domain Archaea were narchaeota) that included the first cultured thermo- actually discovered in the late 18th century (Wolfe, philes in the order Sulfolobales (Brock et al., 1972). 2006) and the first isolates were obtained in the Since then, considerable progress has resulted in the early 20th century (Harrison and Kennedy, 1922; isolation and subsequent genome sequencing of Barker, 1936), these organisms were not recognized numerous thermophiles and hyperthermophiles as a separate lineage from the Bacteria and Eukarya belonging to the Crenarchaeota (Wolfe, 2006). until the groundbreaking work focused on the Characterization of 16S rRNA gene sequences phylogenetics of the 16S rRNA gene (Woese et al., from uncultivated organisms across a myriad of 1976; Woese and Fox, 1977). The newly recognized natural environments as well as isolation of key domain Archaea (Woese et al., 1990) included the reference organisms has expanded our knowledge of the phylogenetic diversity and evolutionary rela- tionships among members of the domain Archaea. Correspondence: WP Inskeep, Department of Land Resources and In fact, phylogenetic placement of deeply rooted Environmental Sciences, Thermal Biology Institute, Montana sequences from Obsidian Pool in Yellowstone State University, PO Box 173120, Bozeman, MT 59717, USA. E-mail: [email protected] National Park (YNP) led to the proposal of a third Received 16 March 2012; revised 10 October 2012; accepted 10 candidate phylum in the mid-1990s, the Korarch- October 2012; published online 15 November 2012 aeota (Barns et al., 1994). Enrichment of Candidatus Geoarchaeota: a new candidate phylum MA Kozubal et al 623 Korarchaeum cryptofilum and subsequent full-gen- lineage (Geoarchaeota) within the domain Archaea. ome analysis provided further evidence that the Analysis of metagenome sequence from replicate Fe- Korarchaeota represent a separate phylum within oxide mat samples (60–78 1C) reveals a dominant the Archaea (Elkins et al., 2008). A fourth phylum archaeal population with novel strategies for energy (Nanoarchaeota) was described after the discovery conservation and oxygen respiration. Evidence is and genome analysis of the symbiont species provided here that these organisms are members of Candidatus Nanoarchaeum equitans (Huber et al., one the earliest currently known lineages of the 2002), although placement of the Nanoarchaeota as a domain Archaea, and that members of this phylum- new phylum is still debated and is based primarily level group are limited primarily to thermophilic on a single genome sequence and 16S rRNA habitats, especially those containing ferrous Fe and sequences (Brochier et al., 2005). More recently, low levels of oxygen. the candidate phylum Thaumarchaeota was pro- posed (Brochier-Armanet et al., 2008), and detailed analysis of genome sequence from multiple represen- Materials and methods tatives of this lineage provides convincing evidence that this group of organisms is significantly different Sample collection and metagenome sequencing from other recognized phyla within the Archaea DNA for metagenome sequencing was extracted (Spang et al., 2010). Specifically, phylogenetic analy- from B10 g of iron-oxide microbial mat from 100 sis of housekeeping genes (that is, ribosomal proteins Spring Plain (Norris Geyser Basin; YNP; (Easting and enzymes involved in translation, replication, 523042/Northing 4953337) sampled at two different cell division and repair) from Nitrosopumilus time points using a FastDNA Spin Kit (MO BIO maritimus, Nitrososphaera gargensis and Candidatus Laboratories, Carlsbad, CA, USA). Environmental Cenarchaeum symbiosum provides strong evidence DNA was precipitated with 3.0 M sodium acetate and for the unique and distinguishing genetic features of 100% ethanol. Sanger sequencing of 3-kb random members of this phylum. The first isolate from this insert pUC18 libraries was used to obtain random group was the ammonia-oxidizing, marine organism shotgun metagenome sequence (average read length B N. maritimus (Ko¨nneke et al., 2005), and this 800 bp) of the first sample obtained in Fall 2007 discovery led to numerous enrichment cultures (OSPB-1). Further replicates sampled 2.4 year after and molecular studies demonstrating the ubiquity OSPB-1 (OSPB-2, OSPC and OSPD) were sequenced of these organisms in various marine settings using 454 titanium pyrosequencing (average read (Hatzenpichler et al., 2008; Walker et al., 2010; length B380 bp; Table 1). Muller et al., 2010; Blainey et al., 2011). Isolates and enrichment cultures from this phylum now include diverse members from marine, soil and hydrother- Metagenome sequence analysis and assembly of NAG1 mal systems (de la Torre et al., 2008; Tourna et al., Random shotgun sequence reads were assembled 2011), and include organisms with novel metabo- using Celera (JCVI) and Newbler (Roche/454, Basel, lisms and/or morphologies, such as the ‘giant’ Switzerland) assemblers. Assembly statistics (coverage, Thaumarchaeota (Muller et al., 2010). The discovery quality scores and GC content) were compiled by the of Thaumarchaeota has resulted in major contribu- Joint Genome Institute (JGI; Walnut Creek, CA, USA). tions to our understanding of global C and N cycling All aspects of library construction and sequencing and the potential importance of CO2 fixation and performed at the JGI can be found at http://www.jgi. nitrification in the open ocean (Ingalls et al., 2006). doe.gov/ including assembly methods, base error and High-temperature environments in YNP have possible mis-assembly corrections. Contigs were further yielded a wealth of knowledge regarding the extant analyzed using nucleotide word frequency (Teeling diversity, distribution and metabolism of archaea et al., 2004) principal component analysis (NWF-PCA) (Barns et al., 1996; Inskeep et al., 2005; Meyer- to separate novel archaeal group 1 (NAG1) contigs Dombard et al., 2005; Inskeep et al., 2010). Previous from other species (performed at http://gos.jcvi.org/ studies of acidic ferric iron mats, in particular, have openAccess/scatterPlotViewer2.html with the follow- shown a remarkable diversity of archaea, which ing parameters: word size ¼ four, minimum contig size corresponds with the combination of unique geo- at 2000 bases, and the chop sequence size at 4000 chemistry and high temperature of these systems bases as described previously for YNP ferric iron mat (Inskeep et al., 2005; Kozubal et al., 2008; Inskeep systems; Inskeep et al., 2010). Further verification of et al., 2010; Kozubal et al., 2012). Prior 16S rRNA NAG1 contigs was obtained by plotting coverage vs gene sequencing of high-temperature (65–80 1C) G þ C content for all metagenome contigs, which acidic
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