DOCSLIB.ORG

This Is an Open Access-Journal's PDF Published in Huntemann, M., Lu, M

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
This Is an Open Access-Journal's PDF Published in Huntemann, M., Lu, M Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH(2)). Item Type Article Authors Huntemann, Marcel; Lu, Megan; Nolan, Matt; Lapidus, Alla; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Ovchinikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Jeffries, Cynthia D; Detter, John C; Brambilla, Evelyne-Marie; Rohde, Manfred; Spring, Stefan; Göker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Mavromatis, Konstantinos Citation Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH(2)). 2011, 4 (3):303-11 Stand Genomic Sci DOI 10.4056/sigs.1814460 Journal Standards in genomic sciences Rights Archived with thanks to Standards in genomic sciences Download date 06/10/2021 02:13:06 Link to Item http://hdl.handle.net/10033/220772 This is an Open Access-journal’s PDF published in Huntemann, M., Lu, M., Nolan, M., Lapidus, A., Lucas, S., Hammon, N., Deshpande, S., Cheng, J.-F., Tapia, R., Han, C., Goodwin, L., Pitluck, S., Liolios, K., Pagani, I., Ivanova, N., Ovchinikova, G., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Jeffries, C.D., Detter, J.C., Brambilla, E.-M., Rohde, M., Spring, S., Göker, M., Woyke, T., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H.-P., Mavromatis, K. Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH2T) (2011) Standards in Genomic Sciences, 4 (3), pp. 303-311 Standards in Genomic Sciences (2011) 4:303-311 DOI:10.4056/sigs.1814460 Complete genome sequence of the thermophilic T sulfur-reducer Hippea maritima type strain (MH2 ) Marcel Huntemann1, Megan Lu2,3, Matt Nolan2, Alla Lapidus2, Susan Lucas2, Nancy Hammon2, Shweta Deshpande2, Jan-Fang Cheng2, Roxanne Tapia2,3, Cliff Han2,3, Lynne Goodwin2,3, Sam Pitluck2, Konstantinos Liolios2, Ioanna Pagani2, Natalia Ivanova2, Galina Ovchinikova2, Amrita Pati2, Amy Chen1, Krishna Palaniappan1, Miriam Land2,4, Loren Hauser2,4, Cynthia D. Jeffries2,4, John C. Detter2,3, Evelyne-Marie Brambilla5, Manfred Rohde6, Stefan Spring5, Markus Göker5, Tanja Woyke2, James Bristow2, Jonathan A. Eisen2,7, Victor Markowitz1, Philip Hugenholtz2,8, Nikos C. Kyrpides2, Hans-Peter Klenk5*, and Konstantinos Mavromatis2 1 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 5 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA 8 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia *Corresponding author: Hans-Peter Klenk Keywords: anaerobic, motile, rod-shaped, Gram-negative, marine, moderately thermophilic, sulfur-reducer, Desulfurellaceae, GEBA Hippea maritima (Miroshnichenko et al. 1999) is the type species of the genus Hippea, which belongs to the family Desulfurellaceae within the class Deltaproteobacteria. The anaerobic, moderately thermophilic marine sulfur-reducer was first isolated from shallow-water hot vents in Matipur Harbor, Papua New Guinea. H. maritima was of interest for genome se- quencing because of its isolated phylogenetic location, as a distant next neighbor of the ge- T nus Desulfurella. Strain MH2 is the first type strain from the order Desulfurellales with a com- pletely sequenced genome. The 1,694,430 bp long linear genome with its 1,723 protein- coding and 57 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. Introduction Strain MH2T (DSM 10411 = ATCC 700847) is the sulfur-reducing bacteria [1]. The genus is named type strain of the species Hippea maritima, which is after the German microbiologist Hans Hippe, in the type species of its genus Hippea [1]. The genus recognition of his significant contribution to the currently contains no other validly named species characterization of novel, obligately anaerobic pro- [2], but two other strains belonging to the species karyotes and the understanding of their physiology. were isolated from shallow-water hot vents in New The species epithet is derived from the Latin word Zealand and Papua New Guinea [1]. The type strain maritima (inhabiting marine environments) [2]. was isolated during a cruise of the Russian scientif- Here we present a summary classification and a set ic vessel A. Nesmeyanov through shallow-water hot of features for H. maritima strain MH2T, together vents of the south-western Pacific Ocean, environ- with the description of the complete genomic se- ments that are typical for anaerobic, thermophilic, quencing and annotation. The Genomic Standards Consortium Hippea maritima type strain (MH2T) Classification and features uses the INSDC (= EMBL/NCBI/DDBJ) annotation, A representative genomic 16S rRNA sequence of which is not an authoritative source for nomencla- ture or classification.) The highest-scoring envi- strain MH2T was compared using NCBI BLAST un- der default settings (e.g., considering only the ronmental sequence was AF232926 ('United high-scoring segment pairs (HSPs) from the best Kingdom: Montserrat geothermal springs clone 250 hits) with the most recent release of the MS10 proteobacterium'), which showed an identi- Greengenes database [3] and the relative frequen- ty of 88.9% and a HSP coverage of 73.0%. The cies, of taxa and keywords (reduced to their stem most frequently occurring keywords within the [4]) were determined, weighted by BLAST scores. labels of environmental samples which yielded The most frequently occurring genera were Desul- hits were 'microbi' (5.0%), 'spring' (2.9%), furella (38.7%), Desulfovibrio (15.2%), Deferribac- 'sediment' (2.4%), 'soil' (2.3%) and 'industri' ter (10.8%), Thermotoga (10.8%) and Hippea (2.2%) (206 hits in total). Environmental samples (8.6%) (44 hits in total). Regarding the single hit which yielded hits of a higher score than the high- to sequences from members of the species, the est scoring species were not found. average identity within HSPs was 99.9%, whereas The 16S rRNA based tree in Figure 1 shows the the average coverage by HSPs was 82.7%. Among phylogenetic neighborhood of H. maritima. The all other species, the one yielding the highest sequence of the two identical 16S rRNA genes dif- score was Desulfurella multipotens, which corres- fers by one nucleotide from the previously pub- ponded to an identity of 89.6% and an HSP cover- lished 16S rRNA sequence (Y18292). age of 82.6%. (Note that the Greengenes database Figure 1. Phylogenetic tree highlighting the position of H. maritima relative to the other type strains within the fam- ily Desulfurellaceae. The tree was inferred from 1,526 aligned characters [5,6] of the 16S rRNA gene sequence under the maximum likelihood criterion [7] and rooted in accordance to the current taxonomy. The branches are scaled in terms of the expected number of substitutions per site. Numbers next to bifurcations are support values from 700 bootstrap replicates [8] if larger than 60%. Lineages with type strain genome sequencing projects regis- tered in GOLD [9] are shown with an asterisk, those also listed as 'Complete and Published' with two asterisks. 304 Standards in Genomic Sciences Huntemann et al. The cells of H. maritima are short rods ranging Harbor, was the only H. maritima strain growing from 1-3 x 0.4–0.8 µm (Figure 2 and Table 1) that on ethanol in the presence of elemental sulfur [1]. occur singly or in pairs [1]. H. maritima is motile Fumarate supported only weak growth for all by one polar flagellum [1] (not visible in Figure 2). three known strains [1], whereas formate, propio- Colonies are whitish-gray with diameters up to 0.5 nate, butyrate, pyruvate, lactate, succinate, glu- mm [1]. H. maritima cultures require 2.5-3% NaCl cose, starch, peptone, methanol did not support and 0.02% (w/v) yeast extract for growth [1]. The growth [1]. CO2 and H2S were the only detected temperature range for growth is between 40°C end products [1]. and 65°C, with an optimum at 52–54°C [1]. Growth was observed over a pH range of 5.7 to 6.5 Chemotaxonomy with an optimum around 6.0 [1]. No chemotaxonomical data were reported in the All H. maritima strains can grow on molecular hy- initial description of the organism [1] nor else- drogen, acetate, and saturated fatty acids and re- where, subsequently. quire elemental sulfur as the only known electron acceptor [1]. Strain MH3, isolated from Matupi T Figure 2. Scanning electron micrograph of H. maritima MH2 http://standardsingenomics.org 305 Hippea maritima type strain (MH2T) T Table 1. Classification and general features of H. maritima MH2 according to the MIGS recommendations [10]. MIGS ID Property Term Evidence code Domain Bacteria TAS [11] Phylum Proteobacteria TAS [12] Class Deltaproteobacteria TAS [13,14] Order Desulfurellales TAS [13,14] Current classification Family Desulfurellaceae TAS [14,15] Genus Hippea TAS [1] Species Hippea maritima TAS [1] Type strain MH2
Load more

Recommended publications
  • Which Organisms Are Used for Anti-Biofouling Studies
    Table S1. Semi-systematic review raw data answering: Which organisms are used for anti-biofouling studies? Antifoulant Method Organism(s) Model Bacteria Type of Biofilm Source (Y if mentioned) Detection Method composite membranes E. coli ATCC25922 Y LIVE/DEAD baclight [1] stain S. aureus ATCC255923 composite membranes E. coli ATCC25922 Y colony counting [2] S. aureus RSKK 1009 graphene oxide Saccharomycetes colony counting [3] methyl p-hydroxybenzoate L. monocytogenes [4] potassium sorbate P. putida Y. enterocolitica A. hydrophila composite membranes E. coli Y FESEM [5] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) K. pneumonia ATCC13883 P. aeruginosa BAA-1744 composite membranes E. coli Y SEM [6] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) graphene oxide E. coli ATCC25922 Y colony counting [7] S. aureus ATCC9144 P. aeruginosa ATCCPAO1 composite membranes E. coli Y measuring flux [8] (unspecified/unique sample type) graphene oxide E. coli Y colony counting [9] (unspecified/unique SEM sample type) LIVE/DEAD baclight S. aureus stain (unspecified/unique sample type) modified membrane P. aeruginosa P60 Y DAPI [10] Bacillus sp. G-84 LIVE/DEAD baclight stain bacteriophages E. coli (K12) Y measuring flux [11] ATCC11303-B4 quorum quenching P. aeruginosa KCTC LIVE/DEAD baclight [12] 2513 stain modified membrane E. coli colony counting [13] (unspecified/unique colony counting sample type) measuring flux S. aureus (unspecified/unique sample type) modified membrane E. coli BW26437 Y measuring flux [14] graphene oxide Klebsiella colony counting [15] (unspecified/unique sample type) P. aeruginosa (unspecified/unique sample type) graphene oxide P. aeruginosa measuring flux [16] (unspecified/unique sample type) composite membranes E.
    [Show full text]
  • 1 Characterization of Sulfur Metabolizing Microbes in a Cold Saline Microbial Mat of the Canadian High Arctic Raven Comery Mast
    Characterization of sulfur metabolizing microbes in a cold saline microbial mat of the Canadian High Arctic Raven Comery Master of Science Department of Natural Resource Sciences Unit: Microbiology McGill University, Montreal July 2015 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of Master in Science © Raven Comery 2015 1 Abstract/Résumé The Gypsum Hill (GH) spring system is located on Axel Heiberg Island of the High Arctic, perennially discharging cold hypersaline water rich in sulfur compounds. Microbial mats are found adjacent to channels of the GH springs. This thesis is the first detailed analysis of the Gypsum Hill spring microbial mats and their microbial diversity. Physicochemical analyses of the water saturating the GH spring microbial mat show that in summer it is cold (9°C), hypersaline (5.6%), and contains sulfide (0-10 ppm) and thiosulfate (>50 ppm). Pyrosequencing analyses were carried out on both 16S rRNA transcripts (i.e. cDNA) and genes (i.e. DNA) to investigate the mat’s community composition, diversity, and putatively active members. In order to investigate the sulfate reducing community in detail, the sulfite reductase gene and its transcript were also sequenced. Finally, enrichment cultures for sulfate/sulfur reducing bacteria were set up and monitored for sulfide production at cold temperatures. Overall, sulfur metabolism was found to be an important component of the GH microbial mat system, particularly the active fraction, as 49% of DNA and 77% of cDNA from bacterial 16S rRNA gene libraries were classified as taxa capable of the reduction or oxidation of sulfur compounds.
    [Show full text]
  • Lake Sediment Microbial Communities in the Anthropocene
    Lake sediment microbial communities in the Anthropocene Matti Olavi Ruuskanen A thesis submitted in partial fulfillment of the requirements for the Doctorate in Philosophy degree in Biology with Specialization in Chemical and Environmental Toxicology Department of Biology Faculty of Science University of Ottawa © Matti Olavi Ruuskanen, Ottawa, Canada, 2019 Abstract Since the Industrial Revolution at the end of the 18th century, anthropogenic changes in the environment have shifted from the local to the global scale. Even remote environments such as the high Arctic are vulnerable to the effects of climate change. Similarly, anthropogenic mercury (Hg) has had a global reach because of atmospheric transport and deposition far from emission point sources. Whereas some effects of climate change are visible through melting permafrost, or toxic effects of Hg at higher trophic levels, the often-invisible changes in microbial community structures and functions have received much less attention. With recent and drastic warming- related changes in Arctic watersheds, previously uncharacterized phylogenetic and functional diversity in the sediment communities might be lost forever. The main objectives of my thesis were to uncover how microbial community structure, functional potential and the evolution of mercury specific functions in lake sediments in northern latitudes (>54ºN) are affected by increasing temperatures and Hg deposition. To address these questions, I examined environmental DNA from sediment core samples and high-throughput sequencing to reconstruct the community composition, functional potential, and evolutionary responses to historical Hg loading. In my thesis I show that the microbial community in Lake Hazen (NU, Canada) sediments is structured by redox gradients and pH. Furthermore, the microbes in this phylogenetically diverse community contain genomic features which might represent adaptations to the cold and oligotrophic conditions.
    [Show full text]
  • Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices
    Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices Jenna Morgan Lang1,2, Aaron E. Darling1, Jonathan A. Eisen1,2* 1 Department of Medical Microbiology and Immunology and Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America, 2 Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America Abstract Over 3000 microbial (bacterial and archaeal) genomes have been made publically available to date, providing an unprecedented opportunity to examine evolutionary genomic trends and offering valuable reference data for a variety of other studies such as metagenomics. The utility of these genome sequences is greatly enhanced when we have an understanding of how they are phylogenetically related to each other. Therefore, we here describe our efforts to reconstruct the phylogeny of all available bacterial and archaeal genomes. We identified 24, single-copy, ubiquitous genes suitable for this phylogenetic analysis. We used two approaches to combine the data for the 24 genes. First, we concatenated alignments of all genes into a single alignment from which a Maximum Likelihood (ML) tree was inferred using RAxML. Second, we used a relatively new approach to combining gene data, Bayesian Concordance Analysis (BCA), as implemented in the BUCKy software, in which the results of 24 single-gene phylogenetic analyses are used to generate a ‘‘primary concordance’’ tree. A comparison of the concatenated ML tree and the primary concordance (BUCKy) tree reveals that the two approaches give similar results, relative to a phylogenetic tree inferred from the 16S rRNA gene. After comparing the results and the methods used, we conclude that the current best approach for generating a single phylogenetic tree, suitable for use as a reference phylogeny for comparative analyses, is to perform a maximum likelihood analysis of a concatenated alignment of conserved, single-copy genes.
    [Show full text]
  • Microbial Distribution in Different Spatial Positions Within the Walls of a Black Sulfide Hydrothermal Chimney
    Vol. 508: 67–85, 2014 MARINE ECOLOGY PROGRESS SERIES Published August 4 doi: 10.3354/meps10841 Mar Ecol Prog Ser Microbial distribution in different spatial positions within the walls of a black sulfide hydrothermal chimney Jiangtao Li1, Huaiyang Zhou1,*, Jiasong Fang1,2,*, Yannan Sun1, Shamik Dasgupta1 1State Key Laboratory of Marine Geology, Tongji University, Shanghai 200092, PR China 2Department of Natural Sciences, Hawaii Pacific University, Kaneohe, Hawaii 96744, USA ABSTRACT: Deep-sea hydrothermal chimneys encompass diverse niches for different micro- bial communities with steep environmental gradients. An active sulfide hydrothermal structure was recovered from the Dudley site of the Main Endeavour Field in the Juan de Fuca Ridge. Subsamples were taken from different spatial positions within the chimney wall and analyzed for mineral composition and microbial biomass and community structure to illustrate the char- acteristics of microbial distribution and environmental constraints. Mineral analysis showed that the chimney was mainly composed of various Fe-, Zn-, and Cu-rich sulfides, with mineral composition and abundance varying with spatial position. Microbial populations in the chimney predominantly consisted of archaeal members affiliated with the deep-sea hydrothermal vent Euryarchaeota group, Thermococcales, and Desulfurococcales, as well as bacterial members of the Gamma-, Epsilon-, and Deltaproteobacteria. Microbial biomass and composition shifted dramatically and formed different microbial zones within the chimney walls, from predomi- nantly mesophilic, sulfur-oxidizing bacterial communities at the outer surfaces to thermophilic or hyperthermophilic, archaeal sulfur-reducers in the inner layers of the chimney. Based on microbial physiological characteristics and their distribution profiles, we inferred that tempera- ture, fluid geochemistry, and organic compounds probably play an important role in selecting for and sustaining microbial communities.
    [Show full text]
  • Phylogenetic Profile of Copper Homeostasis in Deltaproteobacteria
    Phylogenetic Profile of Copper Homeostasis in Deltaproteobacteria A Major Qualifying Report Submitted to the Faculty of Worcester Polytechnic Institute In Partial Fulfillment of the Requirements for the Degree of Bachelor of Science By: __________________________ Courtney McCann Date Approved: _______________________ Professor José M. Argüello Biochemistry WPI Project Advisor 1 Abstract Copper homeostasis is achieved in bacteria through a combination of copper chaperones and transporting and chelating proteins. Bioinformatic analyses were used to identify which of these proteins are present in Deltaproteobacteria. The genetic environment of the bacteria is affected by its lifestyle, as those that live in higher concentrations of copper have more of these proteins. Two major transport proteins, CopA and CusC, were found to cluster together frequently in the genomes and appear integral to copper homeostasis in Deltaproteobacteria. 2 Acknowledgements I would like to thank Professor José Argüello for giving me the opportunity to work in his lab and do some incredible research with some equally incredible scientists. I need to give all of my thanks to my supervisor, Dr. Teresita Padilla-Benavides, for having me as her student and teaching me not only lab techniques, but also how to be scientist. I would also like to thank Dr. Georgina Hernández-Montes and Dr. Brenda Valderrama from the Insituto de Biotecnología at Universidad Nacional Autónoma de México (IBT-UNAM), Campus Morelos for hosting me and giving me the opportunity to work in their lab. I would like to thank Sarju Patel, Evren Kocabas, and Jessica Collins, whom I’ve worked alongside in the lab. I owe so much to these people, and their support and guidance has and will be invaluable to me as I move forward in my education and career.
    [Show full text]
  • Metagenome-Assembled Genomes Provide New Insights Into
    bioRxiv preprint doi: https://doi.org/10.1101/392308; this version posted August 15, 2018. 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. 1 There and back again: metagenome-assembled genomes provide new insights 2 into two thermal pools in Kamchatka, Russia 3 4 Authors: Laetitia G. E. Wilkins1,2#*, Cassandra L. Ettinger2#, Guillaume Jospin2 & 5 Jonathan A. Eisen2,3,4 6 7 Affiliations 8 9 1. Department of Environmental Sciences, Policy & Management, University of 10 California, Berkeley, CA, USA. 11 2. Genome Center, University of California, Davis, CA, USA. 12 3. Department of Evolution and Ecology, University of California, Davis, CA, USA. 13 4. Department of Medical Microbiology and Immunology, University of California, Davis, 14 CA, USA. 15 16 # These authors contributed equally 17 18 *Corresponding author: Laetitia G. E. Wilkins, [email protected], +1-510- 19 643-9688, 304-306 Mulford Hall, University of California, Berkeley, CA, 94720, USA 1 bioRxiv preprint doi: https://doi.org/10.1101/392308; this version posted August 15, 2018. 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. 20 Abstract: 21 22 Culture-independent methods have contributed substantially to our understanding of 23 global microbial diversity.
    [Show full text]
  • Metagenome-Assembled Genomes Provide New Insight Into The
    www.nature.com/scientificreports Corrected: Author Correction OPEN Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal Received: 17 August 2018 Accepted: 17 January 2019 pools in Kamchatka, Russia Published online: 28 February 2019 Laetitia G. E. Wilkins1,2, Cassandra L. Ettinger 2, Guillaume Jospin2 & Jonathan A. Eisen 2,3,4 Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refned, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. We assembled genomes of bacteria and archaea using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and inferred their placement in a phylogenetic tree consisting of 3,240 publicly available microbial genomes. We highlight MAGs that were taxonomically assigned to groups previously underrepresented in available genome data. This includes several archaea (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one potentially new species within the bacterial genus Sulfurihydrogenibium. Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study adds comprehensive information about phylogenetic diversity and functional potential within two hot springs in the caldera of Kamchatka. Terrestrial hydrothermal systems are of great interest to the general public and to scientists alike due to their unique and extreme conditions.
    [Show full text]
  • Metagenome-Assembled Genomes Provide New Insights Into
    bioRxiv preprint doi: https://doi.org/10.1101/392308; this version posted August 15, 2018. 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. 1 There and back again: metagenome-assembled genomes provide new insights 2 into two thermal pools in Kamchatka, Russia 3 4 Authors: Laetitia G. E. Wilkins1,2#*, Cassandra L. Ettinger2#, Guillaume Jospin2 & 5 Jonathan A. Eisen2,3,4 6 7 Affiliations 8 9 1. Department of Environmental Sciences, Policy & Management, University of 10 California, Berkeley, CA, USA. 11 2. Genome Center, University of California, Davis, CA, USA. 12 3. Department of Evolution and Ecology, University of California, Davis, CA, USA. 13 4. Department of Medical Microbiology and Immunology, University of California, Davis, 14 CA, USA. 15 16 # These authors contributed equally 17 18 *Corresponding author: Laetitia G. E. Wilkins, [email protected], +1-510- 19 643-9688, 304-306 Mulford Hall, University of California, Berkeley, CA, 94720, USA 1 bioRxiv preprint doi: https://doi.org/10.1101/392308; this version posted August 15, 2018. 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. 20 Abstract: 21 22 Culture-independent methods have contributed substantially to our understanding of 23 global microbial diversity.
    [Show full text]
  • Microbial Communities and Interactions of Nitrogen Oxides with Methanogenesis in Diverse Peatlands of the Amazon Basin
    Supplementary Material Microbial Communities and Interactions of Nitrogen Oxides With Methanogenesis in Diverse Peatlands of the Amazon Basin S. Buessecker, Z. Zamora, A. F. Sarno, D. R. Finn, A. M. Hoyt, J. van Haren, J. D. Urquiza Muñoz, and H. Cadillo-Quiroz Correspondence to: H. Cadillo-Quiroz ([email protected]) Supplementary Material 1 Supplementary Discussion Dissolved organic carbon (DOC) profiles. DOC has emerged as an important predictor of CH4 production in wetland soils (Liu et al., 2012; Morrissey et al., 2013). In comparison, DOC concentrations obtained in this study are at the lower end of values previously reported from Borneo peats (Gandois et al., 2014). All concentration profiles appear stable along soil depth with no indication of sinks. These would conceivably occur in more shallow regions where the fraction of refractory soil carbon is less prevalent (Artz et al., 2006). A DOC sink due to mineralization is not present based on our data. The DOC pool is comprised of diverse organic molecules characterized by a wide molecular size range, organic acids, humic substances of different aromaticities, and protein groups. These compounds may vary with depth even though the bulk concentration may be stagnant. Extracellular enzymes and humic substances may play a crucial role in diverting electron flow from methanogenesis, given the thermodynamic preference over CO2 (Heitmann et al., 2007; Knorr and Blodau, 2009), that would ultimately suppress CH4 production. Based on our results, we can exclude fluctuations of the total DOC pool to have major effects on carbon mineralization in distinct soil layers, but organic compounds could structurally differ along depth and impact specific microbial activities.
    [Show full text]
  • Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (Phyl. Nov.)
    fmicb-08-00682 April 20, 2017 Time: 17:21 # 1 ORIGINAL RESEARCH published: 24 April 2017 doi: 10.3389/fmicb.2017.00682 Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.) David W. Waite1, Inka Vanwonterghem1, Christian Rinke1, Donovan H. Parks1, Ying Zhang2, Ken Takai3, Stefan M. Sievert4, Jörg Simon5, Barbara J. Campbell6, Thomas E. Hanson7, Tanja Woyke8, Martin G. Klotz9,10 and Philip Hugenholtz1* 1 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia, 2 Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI, USA, 3 Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan, 4 Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA, 5 Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany, 6 Department of Biological Sciences, Life Science Facility, Clemson University, Clemson, SC, USA, 7 School of Marine Science and Policy, College of Earth, Ocean, and Environment, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA, 8 Department of Energy, Joint Genome Institute, Walnut Edited by: Creek, CA, USA, 9 Department of Biology and School of Earth and Environmental Sciences, Queens College of the City Svetlana N. Dedysh, University
    [Show full text]
  • Complex Subsurface Hydrothermal Fluid Mixing at a Submarine Arc Volcano Supports Distinct and Highly Diverse Microbial Communities
    Complex subsurface hydrothermal fluid mixing at a submarine arc volcano supports distinct and highly diverse microbial communities Anna-Louise Reysenbacha,1,2, Emily St. Johna,2, Jennifer Meneghina, Gilberto E. Floresb, Mircea Podarc, Nina Dombrowskid, Anja Spangd,e, Stephane L’Haridonf, Susan E. Humphrisg, Cornel E. J. de Rondeh, Fabio Caratori Tontinih, Maurice Tiveyg, Valerie K. Stuckeri, Lucy C. Stewarth,j, Alexander Diehlk,l, and Wolfgang Bachk,l aCenter for Life in Extreme Environments, Biology Department, Portland State University, Portland, OR 97201; bDepartment of Biology, California State University, Northridge, CA 91330; cBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831; dRoyal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, NL-1790 AB Den Burg, The Netherlands; eDepartment of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden; fCNRS, Institut Français de Recherche pour l’Exploitation de la Mer, Laboratoire de Microbiologie des Environnements Extrêmes, Université de Bretagne Occidentale, F-29280 Plouzané, France; gDepartment of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543; hDepartment of Earth Systems and Resources, GNS Science, Avalon, Lower Hutt 5010, New Zealand; iLaboratories and Collections, GNS Science, Avalon, Lower Hutt 5010, New Zealand; jToha Science, Wellington 6011, New Zealand; kFaculty of Geosciences, University of Bremen, 28359 Bremen, Germany; and lMARUM - Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany Edited by Edward F. DeLong, University of Hawaii at Manoa, Honolulu, HI, and approved November 3, 2020 (received for review September 10, 2020) Hydrothermally active submarine volcanoes are mineral-rich bio- seawater circulation through oceanic crust.
    [Show full text]