DOCSLIB.ORG

Vulcanisaeta Distributa Gen. Nov., Sp. Nov., and Vulcanisaeta Souniana Sp

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Vulcanisaeta Distributa Gen. Nov., Sp. Nov., and Vulcanisaeta Souniana Sp International Journal of Systematic and Evolutionary Microbiology (2002), 52, 1097–1104 DOI: 10.1099/ijs.0.02152-0 Vulcanisaeta distributa gen. nov., sp. nov., and Vulcanisaeta souniana sp. nov., novel hyperthermophilic, rod-shaped crenarchaeotes isolated from hot springs in Japan 1 Japan Collection of Takashi Itoh,1 Ken-ichiro Suzuki1† and Takashi Nakase1,2 Microorganisms, RIKEN (The Institute of Physical and Chemical Research), Author for correspondence: Wako-shi, Saitama Takashi Itoh. Tel: j81 48 467 8440. Fax: j81 48 462 4860. 351-0198, Japan e-mail: ito!jcm.riken.go.jp 2 Laboratory of Microbiology, Department Seventeen strains of rod-shaped, heterotrophic, anaerobic, hyperthermophilic of Applied Biology and crenarchaeotes were isolated from several hot spring areas in eastern Japan, Chemistry, Faculty of Applied Bioscience, Tokyo and eight representative strains were characterized further. Cells of these University of Agriculture, strains were straight to slightly curved rods, 04–06 µm in width. Occasionally, Sakuragaoka 1-1-1, cells were branched or bore spherical bodies at the poles. They grew optimally Setagaya-ku, Tokyo 156-8502, Japan at 85–90 SC and at pH 40–45. They utilized yeast extract, peptone, beef extract, Casamino acids, gelatin, starch, maltose and malate as carbon sources and sulfur and thiosulfate as possible electron acceptors. The DNA GMC contents of the novel isolates were 439–462 mol%. The lipids were mainly cyclic and acyclic tetraether core lipids. Phylogenetic analysis of the 16S rDNA sequences revealed that they represented an independent lineage in the family Thermoproteaceae. Moreover, comparison of the 16S rDNA sequences and a DNA–DNA hybridization study showed that they comprised two species, which could also be differentiated by the maximal growth temperature and degrees of NaCl tolerance. Therefore, a new genus, Vulcanisaeta gen. nov., in the family Thermoproteaceae is proposed to accommodate two novel species, Vulcanisaeta distributa sp. nov. and Vulcanisaeta souniana sp. nov. The type species is V. distributa and the type strains are V. distributa IC-017T (l JCM 11212T l DSM 14429T) and V. souniana IC-059T (l JCM 11219T l DSM 14430T). Keywords: Vulcanisaeta distributa, Vulcanisaeta souniana, Thermoproteaceae, hyperthermophilic Archaea INTRODUCTION proteaceae and Thermofilaceae (Burggraf et al., 1997). They are strict or facultative anaerobes that metabolize All the known species within the kingdom Crenar- sulfur and\or thiosulfate and are reported to be chaeota are obligate thermophiles with maximum distributed widely in terrestrial hot springs and marine growth temperatures ranging from 75 to 113 mC geothermal habitats (Huber & Stetter, 2001). Until (Stetter, 1998). Using 16S rRNA\DNA-based phylo- recently, only a few genera and species had been genetic analysis, they can be divided into three major described in the order Thermoproteales (Bonch-Osmo- clusters that correspond to the orders Desulfurococ- lovskaya et al., 1990; Huber et al., 1987; Vo$ lkl et al., cales, Sulfolobales and Thermoproteales (Ludwig & 1993; Zillig et al., 1981, 1983; Zillig, 1989). However, Klenk, 2001; Reysenbach, 2001). At present, all rod- the recent discoveries of two new genera in the family shaped crenarchaeotes are included in the order Thermoproteaceae (Thermocladium and Caldivirga; Thermoproteales, represented by the families Thermo- Itoh et al., 1998a, 1999) and two novel Pyrobaculum species [Pyrobaculum arsenaticum (Huber et al., 2000) ................................................................................................................................................. and Pyrobaculum oguniense (Sako et al., 2001)], as well † Present address: Biological Resource Center, Biotechnology Center, National Institute of Technology and Evaluation, Kazusa-Kamatari, as the detection of several phylotypes related to Kisarazu, Chiba 292-0812, Japan. members of the order Thermoproteales (Barns et al., The DDBJ accession numbers for the 16S rDNA sequences determined in 1994, 1996; Reysenbach et al., 2000; Takai & Hori- this study are AB063630–AB063647, as detailed in Fig. 2. koshi, 1999), suggest that there may be a wider 02152 # 2002 IUMS Printed in Great Britain 1097 T. Itoh, K. Suzuki and T. Nakase diversity of rod-shaped crenarchaeotes in geothermal at atmospheric pressure. Caldivirga maquilingensis JCM habitats. 10307T was cultivated as a reference strain, as described previously (Itoh et al., 1999). In the course of our exploration for novel thermophilic Archaea inhabiting terrestrial geothermal habitats, we Phenotypic and genetic studies. Morphology, growth have isolated a number of thermophilic organisms characteristics, utilization of carbon sources, possible elec- from hot springs in Japan and the Philippines. A tron acceptors, antibiotic sensitivity, lipid composition, preliminary grouping of the rod-shaped isolates by the DNA base composition and DNA–DNA relatedness were ability to grow at 85 mC, DNA base composition and determined as described previously (Itoh et al., 1998a). partial 16S rDNA sequences revealed the existence of Morphology, growth characteristics and utilization of car- another unassigned group belonging to the family bon sources were studied using the medium described above. Thermoproteaceae For electron microscopy, cells were placed on a collodion- , in addition to groups correspond- coated grid, shadowed with platinum\palladium and ex- ing to the genera Caldivirga, Thermocladium and amined with a transmission electron microscope (H-300; Thermoproteus (T. Itoh, K. Suzuki, P. C. Sanchez and Hitachi). Possible electron acceptors were identified using a T. Nakase, unpublished). This paper describes the test medium (Itoh et al., 1998a) under a N# atmosphere. isolation and characterization of a novel group of Growth was estimated by fluorescence intensities after organisms in the family Thermoproteaceae and pro- treatment with NanoOrange dye (Molecular Probes) ac- poses a new genus, Vulcanisaeta gen. nov., including cording to the supplier’s protocol or direct counting using a two novel species, Vulcanisaeta distributa sp. nov. and Petroff-Hauser counting chamber (0n02 mm in depth). A Vulcanisaeta souniana sp. nov. good correlation between the two methods was obtained. 16S rDNA sequencing and phylogenetic analysis were METHODS conducted as reported previously (Itoh et al., 1999). 16S rDNA was amplified with primers A-20F (5h-TCCGGTTG- Isolation procedure. Samples of hot-spring water, mud and ATCCTGCCG-3h, corresponding to positions 8–24 in the soil were collected from several hot spring sites in Japan in Escherichia coli numbering system) and A-1530R (5h-GGA- 1993 and 1994 (Table 1). The samples were transported in GGTGATCCAGCCG-3h, positions 1540–1525). Partial 16S sterile plastic tubes without temperature control and were rDNA sequences were determined with a sequencing primer inoculated within 3 days of sampling into an enrichment A-690R (5h-GGATTTCRCCCCTAC-3h, positions 699– medium described previously (Itoh et al., 1998a) at pH 685). In addition, almost complete 16S rDNA sequences of values ranging from 3n5to6n0. The cultures were incubated five novel isolates and Pyrobaculum organotrophum JCM at 85 mC under N# at atmospheric pressure. After 1 week of 9190T were determined in this study. The 16S rDNA cultivation, cultures yielding predominantly rod-shaped cells sequences were aligned first on the program were purified by the serial dilution technique, as described (Thompson et al., 1997) and edited manually with the aid of previously (Itoh et al., 1998a). the SSU rRNA database (Van de Peer et al., 2000). Culture conditions. The isolates were routinely cultivated in Evolutionary distances were calculated after gaps, ambigu- the salt base solution of the Sulfolobus medium (Brock et al., ous bases and unalignable regions had been eliminated. The " " 1972), containing 0n5 g yeast extract l− ,1n0 mg resazurin l− , phylogenetic tree was constructed by the neighbour-joining −" −" 0n5gNa#S.9H#Ol and 10n0 g sulfur l ,pH4n0–4n5 (adjust- method (Saitou & Nei, 1987) and was evaluated by bootstrap ed at room temperature). N# was used as the gas phase sampling (Felsenstein, 1985). Table 1. Sources of novel isolates ................................................................................................................................................................................................................................................................................................................. Strains identified as Thermoproteus spp. are underlined. All locations are in east Japan (prefectures are shown after commas). The pH of the samples was determined at room temperature. , Not determined. Isolate(s) Location Sample Temperature (mC) pH Date IC-017T, IC-019 Ohwakudani, Kanagawa Water 2n0–2n509\1993 IC-058 Ohwakudani, Kanagawa Soil 85 2n702\1994 IC-051, IC-064 Ohwakudani, Kanagawa Soil 90 1n402\1994 IC-052, IC-065 Ohwakudani, Kanagawa Soil 90 2n102\1994 IC-059T, IC-060, IC-061, IC-062 Sounzan, Kanagawa Water 3n0–3n202\1994 IC-029 Okushiobara, Tochigi Soil 90 1n211\1993 IC-030 Okushiobara, Tochigi Soil 90 3n011\1993 IC-031 Okushiobara, Tochigi Water 75 2n911\1993 IC-032 Okushiobara, Tochigi Water 85 3n411\1993 IC-135 Tamagawa, Akita Water 90 1n611\1994 IC-141 Tamagawa, Akita Water 65 1n811\1994 IC-124 Fukenoyu, Akita Water 90 2n411\1994 IC-136 Gosyokake, Akita Soil 65 2n511\1994 IC-140 Ohnuma, Akita Mud 75 3n311\1994 1098 International Journal of Systematic and Evolutionary
Load more

Recommended publications
  • Developing a Genetic Manipulation System for the Antarctic Archaeon, Halorubrum Lacusprofundi: Investigating Acetamidase Gene Function
    www.nature.com/scientificreports OPEN Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: Received: 27 May 2016 Accepted: 16 September 2016 investigating acetamidase gene Published: 06 October 2016 function Y. Liao1, T. J. Williams1, J. C. Walsh2,3, M. Ji1, A. Poljak4, P. M. G. Curmi2, I. G. Duggin3 & R. Cavicchioli1 No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms.
    [Show full text]
  • Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma Divulgatum
    microorganisms Article Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum Rafael Bargiela 1 , Karin Lanthaler 1,2, Colin M. Potter 1,2 , Manuel Ferrer 3 , Alexander F. Yakunin 1,2, Bela Paizs 1,2, Peter N. Golyshin 1,2 and Olga V. Golyshina 1,2,* 1 School of Natural Sciences, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK; [email protected] (R.B.); [email protected] (K.L.); [email protected] (C.M.P.); [email protected] (A.F.Y.); [email protected] (B.P.); [email protected] (P.N.G.) 2 Centre for Environmental Biotechnology, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK 3 Systems Biotechnology Group, Department of Applied Biocatalysis, CSIC—Institute of Catalysis, Marie Curie 2, 28049 Madrid, Spain; [email protected] * Correspondence: [email protected]; Tel.: +44-1248-388607; Fax: +44-1248-382569 Received: 27 April 2020; Accepted: 15 May 2020; Published: 19 May 2020 Abstract: The archaeon Cuniculiplasma divulgatum is ubiquitous in acidic environments with low-to-moderate temperatures. However, molecular mechanisms underlying its ability to thrive at lower temperatures remain unexplored. Using mass spectrometry (MS)-based proteomics, we analysed the effect of short-term (3 h) exposure to cold. The C. divulgatum genome encodes 2016 protein-coding genes, from which 819 proteins were identified in the cells grown under optimal conditions. In line with the peptidolytic lifestyle of C. divulgatum, its intracellular proteome revealed the abundance of proteases, ABC transporters and cytochrome C oxidase. From 747 quantifiable polypeptides, the levels of 582 proteins showed no change after the cold shock, whereas 104 proteins were upregulated suggesting that they might be contributing to cold adaptation.
    [Show full text]
  • Pyrobaculum Igneiluti Sp. Nov., a Novel Anaerobic Hyperthermophilic Archaeon That Reduces Thiosulfate and Ferric Iron
    TAXONOMIC DESCRIPTION Lee et al., Int J Syst Evol Microbiol 2017;67:1714–1719 DOI 10.1099/ijsem.0.001850 Pyrobaculum igneiluti sp. nov., a novel anaerobic hyperthermophilic archaeon that reduces thiosulfate and ferric iron Jerry Y. Lee, Brenda Iglesias, Caleb E. Chu, Daniel J. P. Lawrence and Edward Jerome Crane III* Abstract A novel anaerobic, hyperthermophilic archaeon was isolated from a mud volcano in the Salton Sea geothermal system in southern California, USA. The isolate, named strain 521T, grew optimally at 90 C, at pH 5.5–7.3 and with 0–2.0 % (w/v) NaCl, with a generation time of 10 h under optimal conditions. Cells were rod-shaped and non-motile, ranging from 2 to 7 μm in length. Strain 521T grew only in the presence of thiosulfate and/or Fe(III) (ferrihydrite) as terminal electron acceptors under strictly anaerobic conditions, and preferred protein-rich compounds as energy sources, although the isolate was capable of chemolithoautotrophic growth. 16S rRNA gene sequence analysis places this isolate within the crenarchaeal genus Pyrobaculum. To our knowledge, this is the first Pyrobaculum strain to be isolated from an anaerobic mud volcano and to reduce only either thiosulfate or ferric iron. An in silico genome-to-genome distance calculator reported <25 % DNA–DNA hybridization between strain 521T and eight other Pyrobaculum species. Due to its genotypic and phenotypic differences, we conclude that strain 521T represents a novel species, for which the name Pyrobaculum igneiluti sp. nov. is proposed. The type strain is 521T (=DSM 103086T=ATCC TSD-56T). Anaerobic respiratory processes based on the reduction of recently revealed by the receding of the Salton Sea, ejects sulfur compounds or Fe(III) have been proposed to be fluid of a similar composition at 90–95 C.
    [Show full text]
  • Differences in Lateral Gene Transfer in Hypersaline Versus Thermal Environments Matthew E Rhodes1*, John R Spear2, Aharon Oren3 and Christopher H House1
    Rhodes et al. BMC Evolutionary Biology 2011, 11:199 http://www.biomedcentral.com/1471-2148/11/199 RESEARCH ARTICLE Open Access Differences in lateral gene transfer in hypersaline versus thermal environments Matthew E Rhodes1*, John R Spear2, Aharon Oren3 and Christopher H House1 Abstract Background: The role of lateral gene transfer (LGT) in the evolution of microorganisms is only beginning to be understood. While most LGT events occur between closely related individuals, inter-phylum and inter-domain LGT events are not uncommon. These distant transfer events offer potentially greater fitness advantages and it is for this reason that these “long distance” LGT events may have significantly impacted the evolution of microbes. One mechanism driving distant LGT events is microbial transformation. Theoretically, transformative events can occur between any two species provided that the DNA of one enters the habitat of the other. Two categories of microorganisms that are well-known for LGT are the thermophiles and halophiles. Results: We identified potential inter-class LGT events into both a thermophilic class of Archaea (Thermoprotei) and a halophilic class of Archaea (Halobacteria). We then categorized these LGT genes as originating in thermophiles and halophiles respectively. While more than 68% of transfer events into Thermoprotei taxa originated in other thermophiles, less than 11% of transfer events into Halobacteria taxa originated in other halophiles. Conclusions: Our results suggest that there is a fundamental difference between LGT in thermophiles and halophiles. We theorize that the difference lies in the different natures of the environments. While DNA degrades rapidly in thermal environments due to temperature-driven denaturization, hypersaline environments are adept at preserving DNA.
    [Show full text]
  • Abstract Straub, Christopher Thomas
    ABSTRACT STRAUB, CHRISTOPHER THOMAS. Metabolic Engineering of Extreme Thermophiles for Conversion of Renewable Feedstocks to Industrial Chemicals (Under the direction of Dr. Robert M. Kelly.) Extremely thermophilic microorganisms (Topt 70°C) challenge assumptions about the origins and limits of life. The diverse and specialized biological machinery, mechanisms, and systems utilized by these microorganisms ensure that these bacteria and archaea thrive in extreme thermal environments. These facets can be exploited for contributions to biotechnology in the pursuit of renewable, sustainable, and environmentally compatible solutions to needs for energy and materials. Caldicellulosiruptor bescii is an anaerobic bacterium that was isolated from thermal hot springs. It grows optimally at 78°C (172°F) on plant matter that has washed into the hot springs in which it resides. C. bescii natively deconstructs and ferments the cellulose and hemi-cellulose primarily to acetate, CO2 and H2. C. bescii has previously been shown to utilize approximately 30% of the available carbohydrate content in biomass, limited by the complex network of lignocellulosic biomass. However, by implementation of a mild sodium hydroxide pretreatment, C. bescii metabolized 70% of the carbohydrate content of pretreated switchgrass. Wild-type and transgenic black cottonwood (Populus trichocarpa) were also evaluated as feedstocks for C. bescii conversion. With milled wild-type poplar, C. bescii converted only 25% of the carbohydrate content, in contrast to nearly 90% of the carbohydrate content of a low lignin transgenic line created by down-regulation of the coumarate-3-hydroxylase (C3H3) gene. Furthermore, when entire stem samples of the transgenic line were utilized without milling, C. bescii solubilized over 50% of the feedstock, which has important biotechnological and economic consequences.
    [Show full text]
  • Occurrence and Expression of Novel Methyl-Coenzyme M Reductase Gene
    www.nature.com/scientificreports OPEN Occurrence and expression of novel methyl-coenzyme M reductase gene (mcrA) variants in hot spring Received: 6 April 2017 Accepted: 27 June 2017 sediments Published: xx xx xxxx Luke J. McKay1,2, Roland Hatzenpichler1,3, William P. Inskeep2 & Matthew W. Fields1,4 Recent discoveries have shown that the marker gene for anaerobic methane cycling (mcrA) is more widespread in the Archaea than previously thought. However, it remains unclear whether novel mcrA genes associated with the Bathyarchaeota and Verstraetearchaeota are distributed across diverse environments. We examined two geochemically divergent but putatively methanogenic regions of Yellowstone National Park to investigate whether deeply-rooted archaea possess and express novel mcrA genes in situ. Small-subunit (SSU) rRNA gene analyses indicated that Bathyarchaeota were predominant in seven of ten sediment layers, while the Verstraetearchaeota and Euryarchaeota occurred in lower relative abundance. Targeted amplifcation of novel mcrA genes suggested that diverse taxa contribute to alkane cycling in geothermal environments. Two deeply-branching mcrA clades related to Bathyarchaeota were identifed, while highly abundant verstraetearchaeotal mcrA sequences were also recovered. In addition, detection of SSU rRNA and mcrA transcripts from one hot spring suggested that predominant Bathyarchaeota were also active, and that methane cycling genes are expressed by the Euryarchaeota, Verstraetearchaeota, and an unknown lineage basal to the Bathyarchaeota. These fndings greatly expand the diversity of the key marker gene for anaerobic alkane cycling and outline the need for greater understanding of the functional capacity and phylogenetic afliation of novel mcrA variants. Archaea are the primary drivers of CH4 cycling on our planet.
    [Show full text]
  • Ammonia-Oxidizing Archaea Use the Most Energy Efficient Aerobic Pathway for CO2 Fixation
    Ammonia-oxidizing archaea use the most energy efficient aerobic pathway for CO2 fixation Martin Könneke, Daniel M. Schubert, Philip C. Brown, Michael Hügler, Sonja Standfest, Thomas Schwander, Lennart Schada von Borzyskowski, Tobias J. Erb, David A. Stahl, Ivan A. Berg Supporting Information: Supplementary Appendix SI Text Phylogenetic analysis of the proteins involved in the HP/HB cycle in N. maritimus. The enzymes of the HP/HB cycle with unequivocally identified genes consisting of more than 200 amino acids were used for the phylogenetic analysis (Table 1). The genes for biotin carrier protein (Nmar_0274, 140 amino acids), small subunit of methylmalonyl-CoA mutase (Nmar_0958, 140 amino acids) and methylmalonyl-CoA epimerase (Nmar_0953, 131 amino acids) were not analyzed, because their small size prevents reliable phylogenetic tree construction. The genes for acetyl-CoA/propionyl-CoA carboxylase and methylmalonyl-CoA carboxylase homologues can be found in autotrophic Thaumarchaeota and aerobic Crenarchaeota as well as in some heterotrophic Archaea (SI Appendix, Figs. S7-S9, Table S4). Although these enzymes are usually regarded as characteristic enzymes of the HP/HB cycle, they also participate in various heterotrophic pathways in Archaea, e.g. in the methylaspartate cycle of acetate assimilation in haloarchaea (1), propionate and leucine assimilation (2, 3), oxaloacetate or methylmalonyl-CoA decarboxylation (4, 5), anaplerotic pyruvate carboxylation (6). In all three trees (SI Appendix, Figs. S7-S9) the crenarchaeal enzymes tend to cluster with thaumarchaeal ones, but there appears to be no special connection between aerobic Crenarchaeota (Sulfolobales) and Thaumarchaeota sequences. Thaumarchaeal 4-hydroxybutyryl-CoA dehydratase genes form a separate cluster closely related to bacterial sequences; the bacterial enzymes are probably involved in aminobutyrate fermentation (Fig.
    [Show full text]
  • 4 Metabolic and Taxonomic Diversification in Continental Magmatic Hydrothermal Systems
    Maximiliano J. Amenabar, Matthew R. Urschel, and Eric S. Boyd 4 Metabolic and taxonomic diversification in continental magmatic hydrothermal systems 4.1 Introduction Hydrothermal systems integrate geological processes from the deep crust to the Earth’s surface yielding an extensive array of spring types with an extraordinary diversity of geochemical compositions. Such geochemical diversity selects for unique metabolic properties expressed through novel enzymes and functional characteristics that are tailored to the specific conditions of their local environment. This dynamic interaction between geochemical variation and biology has played out over evolu- tionary time to engender tightly coupled and efficient biogeochemical cycles. The timescales by which these evolutionary events took place, however, are typically in- accessible for direct observation. This inaccessibility impedes experimentation aimed at understanding the causative principles of linked biological and geological change unless alternative approaches are used. A successful approach that is commonly used in geological studies involves comparative analysis of spatial variations to test ideas about temporal changes that occur over inaccessible (i.e. geological) timescales. The same approach can be used to examine the links between biology and environment with the aim of reconstructing the sequence of evolutionary events that resulted in the diversity of organisms that inhabit modern day hydrothermal environments and the mechanisms by which this sequence of events occurred. By combining molecu- lar biological and geochemical analyses with robust phylogenetic frameworks using approaches commonly referred to as phylogenetic ecology [1, 2], it is now possible to take advantage of variation within the present – the distribution of biodiversity and metabolic strategies across geochemical gradients – to recognize the extent of diversity and the reasons that it exists.
    [Show full text]
  • A K-MER PAINTING APPROACH for METAGENOMIC TAXONOMIC PROFILING and QUANTIFICATION of NOVEL STRAIN VARIATION
    bioRxiv preprint doi: https://doi.org/10.1101/039909; this version posted February 17, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. METAPALETTE: A k-MER PAINTING APPROACH FOR METAGENOMIC TAXONOMIC PROFILING AND QUANTIFICATION OF NOVEL STRAIN VARIATION. DAVID KOSLICKI1∗, DANIEL FALUSH2 1Mathematics Department, Oregon State University, Corvallis, OR 97330 2 Institute of Life Sciences, University of Swansea, Singleton Park, Swansea, SA2 8PP UK Abstract. Metagenomic profiling is challenging in part because of the highly uneven sampling of the tree of life by genome sequencing projects and the limitations imposed by performing phy- logenetic inference at fixed taxonomic ranks. We present the algorithm MetaPalette which uses long k-mer sizes (k = 30; 50) to fit a k-mer \palette" of a given sample to the k-mer palette of reference organisms. By modeling the k-mer palettes of unknown organisms, the method also gives an indication of the presence, abundance, and evolutionary relatedness of novel organisms present in the sample. The method returns a traditional, fixed-rank taxonomic profile which is shown on independently simulated data to be one of the most accurate to date. Tree figures are also returned that quantify the relatedness of novel organisms to reference sequences and the accuracy of such figures is demonstrated on simulated spike-ins and a metagenomic soil sample. The software implementing MetaPalette is available at: https://github.com/dkoslicki/MetaPalette Pre-trained databases are included for Archaea, Bacteria, Eukaryota, and viruses.
    [Show full text]
  • A Genome Compendium Reveals Diverse Metabolic Adaptations of Antarctic Soil Microorganisms
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.06.239558; this version posted August 6, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. August 3, 2020 A genome compendium reveals diverse metabolic adaptations of Antarctic soil microorganisms Maximiliano Ortiz1 #, Pok Man Leung2 # *, Guy Shelley3, Marc W. Van Goethem1,4, Sean K. Bay2, Karen Jordaan1,5, Surendra Vikram1, Ian D. Hogg1,7,8, Thulani P. Makhalanyane1, Steven L. Chown6, Rhys Grinter2, Don A. Cowan1 *, Chris Greening2,3 * 1 Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria 0002, South Africa 2 Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia 3 School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia 4 Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 6 Securing Antarctica’s Environmental Future, School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia 7 School of Science, University of Waikato, Hamilton 3240, New Zealand 8 Polar Knowledge Canada, Canadian High Arctic Research Station, Cambridge Bay, NU X0B 0C0, Canada # These authors contributed equally to this work. * Correspondence may be addressed to: A/Prof Chris Greening ([email protected]) Prof Don A. Cowan ([email protected]) Pok Man Leung ([email protected]) bioRxiv preprint doi: https://doi.org/10.1101/2020.08.06.239558; this version posted August 6, 2020.
    [Show full text]
  • Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages Between Metabolic Potential and Geochemistry
    ORIGINAL RESEARCH ARTICLE published: 15 May 2013 doi: 10.3389/fmicb.2013.00095 Phylogenetic and functional analysis of metagenome sequence from high-temperature archaeal habitats demonstrate linkages between metabolic potential and geochemistry William P.Inskeep 1,2*, Zackary J. Jay 1, Markus J. Herrgard 3, Mark A. Kozubal 1, Douglas B. Rusch4, Susannah G.Tringe 5, Richard E. Macur 1, Ryan deM. Jennings 1, Eric S. Boyd 2,6, John R. Spear 7 and Francisco F. Roberto8 1 Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA 2 Thermal Biology Institute, Montana State University, Bozeman, MT, USA 3 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark 4 Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, USA 5 Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA 6 Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA 7 Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA 8 Newmont Mining Corporation, Englewood, CO, USA Edited by: Geothermal habitats in Yellowstone National Park (YNP) provide an unparalleled opportu- Martin G. Klotz, University of North nity to understand the environmental factors that control the distribution of archaea in Carolina at Charlotte, USA thermal habitats. Here we describe, analyze, and synthesize metagenomic and geochem- Reviewed by: Ivan Berg, Albert-Ludwigs-Universität ical data collected from seven high-temperature
    [Show full text]
  • University of Oklahoma Graduate College
    UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE METABOLITE-PROFILING TO ASSESS IN SITU ANAEROBIC MICROBIAL HYDROCARBON DEGRADATION IN DIVERSE ENVIRONMENTS A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By VICTORIA ALEXANDRA PARISI Norman, Oklahoma 2010 METABOLITE-PROFILING TO ASSESS IN SITU ANAEROBIC MICROBIAL HYDROCARBON DEGRADATION IN DIVERSE ENVIRONMENTS A DISSERTATION APPROVED FOR THE DEPARTMENT OF BOTANY AND MICROBIOLOGY BY __________________________ Dr. Joseph M. Suflita, Chair __________________________ Dr. Lee R. Krumholz __________________________ Dr. Paul A. Lawson __________________________ Dr. Michael J. McInerney __________________________ Dr. Mark A. Nanny Copyright by VICTORIA ALEXANDRA PARISI 2010 All Rights Reserved. Dedication I dedicate this work to my parents, Kim and Don Broomhall. I would not be half the person I am today, without your unconditional love and support. Acknowledgements I would like to thank Dr. Joseph M. Sulfita, my advisor. You have been instrumental in my growth as a young scientist, and will still be an important part of the researcher I have yet to become. I have been afforded opportunities that have encompassed more than I could have ever hoped for. Beyond the lab, you and Taylor also provided me with a home away from home when needed with food, volleyball and lots of advice. I would also thank my committee members for their advisement and guidance in my career at OU: Dr. Lee R. Krumholz, Dr. Paul A. Lawson, Dr. Michael J. McInerney and Dr. Mark A. Nanny, I am grateful for all you have taught me. I appreciated not only your insight with respect to my coursework, but my research as well.
    [Show full text]