DOCSLIB.ORG

Cluster 1 Cluster 3 Cluster 2

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Cluster 1 Cluster 3 Cluster 2 5 9 Luteibacter yeojuensis strain SU11 (Ga0078639_1004, 2640590121) 7 0 Luteibacter rhizovicinus DSM 16549 (Ga0078601_1039, 2631914223) 4 7 Luteibacter sp. UNCMF366Tsu5.1 (FG06DRAFT_scaffold00001.1, 2595447474) 5 5 Dyella japonica UNC79MFTsu3.2 (N515DRAFT_scaffold00003.3, 2558296041) 4 8 100 Rhodanobacter sp. Root179 (Ga0124815_151, 2699823700) 9 4 Rhodanobacter sp. OR87 (RhoOR87DRAFT_scaffold_21.22, 2510416040) Dyella japonica DSM 16301 (Ga0078600_1041, 2640844523) Dyella sp. OK004 (Ga0066746_17, 2609553531) 9 9 9 3 Xanthomonas fuscans (007972314) 100 Xanthomonas axonopodis (078563083) 4 9 Xanthomonas oryzae pv. oryzae KACC10331 (NC_006834, 637633170) 100 100 Xanthomonas albilineans USA048 (Ga0078502_15, 2651125062) 5 6 Xanthomonas translucens XT123 (Ga0113452_1085, 2663222128) 6 5 Lysobacter enzymogenes ATCC 29487 (Ga0111606_103, 2678972498) 100 Rhizobacter sp. Root1221 (056656680) Rhizobacter sp. Root1221 (Ga0102088_103, 2644243628) 100 Aquabacterium sp. NJ1 (052162038) Aquabacterium sp. NJ1 (Ga0077486_101, 2634019136) Uliginosibacterium gangwonense DSM 18521 (B145DRAFT_scaffold_15.16, 2515877853) 9 6 9 7 Derxia lacustris (085315679) 8 7 Derxia gummosa DSM 723 (H566DRAFT_scaffold00003.3, 2529306053) 7 2 Ideonella sp. B508-1 (I73DRAFT_BADL01000387_1.387, 2553574224) Zoogloea sp. LCSB751 (079432982) PHB-accumulating bacterium (PHBDraf_Contig14, 2502333272) Thiobacillus sp. 65-1059 (OJW46643.1) 8 4 Dechloromonas aromatica RCB (NC_007298, 637680051) 8 4 7 7 Dechloromonas sp. JJ (JJ_JJcontig4, 2506671179) Dechloromonas RCB 100 Azoarcus sp. KH32C (AP012304, 2563613793) Dechlorobacter hydrogenophilus LT-1 (LT1_c1, 2508501393) Candidatus Accumulibacter aalborgensis (SBT06972) 4 7 8 1 Methylovorus sp. MP688 chromosome (NC_014733, 649772731) 100 Methylotenera sp. G11 (GQ51DRAFT_unitig_0_quiver_dupTrim_10755.1, 2585895491) Methylotenera sp. 301 chromosome (NC_014207, 646831074) 100 Azoarcus sp. KH32C (AP012304, 2563611812) Azoarcus sp. KH32C (083903159) Prosthecomicrobium hirschii ATCC 27832 (Phi_scaffold00167, 2502379653) 100 Sinobacter flavus DSM 18980 (K343DRAFT_scaffold00006.6, 2527007432) 100 Singularimonas variicoloris DSM 15731 (H149DRAFT_scaffold00002.2, 2521804426) Solimonas aquatica DSM 25927 (Ga0070002_110, 2616681780) Nevskia ramosa DSM 11499 (G513DRAFT_scaffold00001.1, 2523410377) Erythrobacter sp. SG61-1L (Ga0100685_13, 2649615031) 100 Rhodanobacter thiooxydans LCS2 (AJXW01000032, 2538844664) 9 8 Rhodanobacter sp. 2APBS1 (R2APBS1_Contig319, 2506719248) 6 6 Rhodanobacter spathiphylli B39 (AJXT01000032, 2538834093) 9 2 Frateuria terrea CGMCC 1.7053 (IQ04DRAFT_scaffold00001.1, 2599169283) 4 8 100 Dyella ginsengisoli LA-4 (C693DRAFT_AMSF01000010_1.10, 2553029806) 7 3 Dyella thiooxydans ATSB10 (Ga0133357_11, 2687581785) 8 0 Dyella jiangningensis (038623940) 9 4 Rhodanobacter sp. C06 (OOG37668) 9 4 Rhodanobacter sp. B05 (077514108) 9 9 100 Rhodanobacter sp. C01 (077439889) Rudaea cellulosilytica DSM 22992 (F455DRAFT_scaffold00002.2, 2519940479) 100 Rhodanobacter sp. OR444 (RHOOR444DRAFT_NODE_26_len_4038_cov_467_575531.26, 2522338571) 9 0 Rhodanobacter sp. FW510-R12 (RhoFW510R12_5064.2546, 2585805519) 6 4 Thiomonas intermedia K12 chromosome (NC_014153, 646800198) 100 100 Thiomonas sp. str. 3As (FP475956, 651255703) 4 6 Thiomonas sp. CB2 (CDW96384) 100 Thiomonas bhubaneswarensis DSM 18181 (Ga0061069_103, 2616226325) 9 1 Thiomonas sp. FB-6, DSM 25805 (D466DRAFT_scaffold00001.1) Thiomonas 100 Thiomonas sp. FB-Cd, DSM 25617 (CD04DRAFT_scf7180000000014_quiver_quiver.5) Mizugakiibacter sediminis (GAP65883) 9 2 Novosphingobium sp. FSW06-99 (067617120) 100 Novosphingobium acidiphilum DSM 19966 (G404DRAFT_scaffold00003.3, 2523703545) 100 Novosphingobium sp. Fuku2-ISO-50 (067744063) 100 Novosphingobium naphthalenivorans (067734630) 9 7 Novosphingobium malaysiense (052223625) 7 4 Novosphingobium fuchskuhlense (067906227) Composite genome from Trout Bog Hypolimnion pan-assembly TBhypo.metabat.6717 (TH6717DRAFT_TBhypo_metabat_6717_10034064.36, 2583043224) 9 8 Alphaproteobacteria bacterium 64-11 (BGN85_02655, OJU07810) 7 6 9 8 Rhodopila sp. LVNP (Ga0132156_11, 2685829211) 4 6 100 Rhodopila sp. LVNP (Ga0132156_11, 2685831528) Acidisphaera rubrifaciens (048860060) Acetobacteraceae bacterium SCN 69-10 (ABS99_01785, ODU61985) 4 5 Bradyrhizobium lablabi GAS522 (Ga0132013_11, 2694655162) 8 1 Bradyrhizobium erythrophlei (074278193) 9 9 Bradyrhizobium erythrophlei GAS478 (Ga0132009_11, 2700926766) 9 9 9 2 Bradyrhizobium erythrophlei (074278395) 5 0 Bradyrhizobium erythrophlei GAS478 (Ga0132009_11, 2700928529) Bradyrhizobium sp. SEMIA 6208 (Ga0081870_1119, 2636530532) Bradyrhizobium erythrophlei GAS138 (Ga0131997_11, 2698418960) 4 7 Bradyrhizobium sp. STM 3843 (Ga0040047_gi365424980.24, 2597911083) 100 Bradyrhizobium sp. STM 3809 (NZ_CAFJ01000175, 2514440204) Bradyrhizobium sp. Gha (Ga0075231_103, 2653887682) 9 9 Bradyrhizobium sp. ORS278 (NC_009445, BRADO6286) 100 Rhodopseudomonas palustris WS17 (RPWS17_WS17_contig_153.153, RPWS17_04972) 9 2 Rhodopseudomonas palustris S55 (RPS55_01659) 100 100 Rhodopseudomonas palustris ATH 2.1.6, ATCC 17001 (RPATCC17001_02806) Rhodopseudomonas pseudopalustris DSM 123 (Ga0121172_103, 2671915913) 9 6 9 9 Rhodopseudomonas palustris BisB5 (NC_007958, 637963819) Bradyrhizobium sp. STM 3843 (Ga0040047_gi365421839.167, 2597913977) 100 Methylocapsa palsarum NE2 (Ga0116912_132, 2676342706) 100 Methylocapsa acidiphila B2 (MetacDRAFT_Scaffold1.2, 2510255561) Methylocystis bryophila (085771681) 7 6 Methylobacter sp. BBA5.1 (EK22DRAFT_scaffold00011.11, 2582536956) 9 6 Aerobic methanotroph, WIN4C from tailings pond WIP (PD1; 2522717648) 100 8 1 Methylobacter luteus IMV-B-3098T (MetluDRAFT_scaffold2.2, 2517428901) Methylobacter tundripaludum SV96 ctg233 (NZ_AEGW01000005, 648843130) 9 9 Composite genome from Trout Bog Epilimnion pan-assembly TBepi.metabat.5136 (TE5136DRAFT_TBepi_metabat_5136_1002297.139, 2582885061) 9 1 Methylococcaceae-21 (UID203) (Ga0081623_1188, 2634877808) 5 8 Methylovulum miyakonense HT12 (MetmiDRAFT_scaffold1.1, 2516960547) Methylococaceae sp. 73a (EK23DRAFT_scaffold00012.12, 2585139763) 100 Methylomonas sp. LWB (083386236) 100 Methylomonas koyamae (082885624) 100 Methylomonas scaffold9 (2574134454) 100 Methylomonas sp. 11b (scaffold1, 2516190406) 9 2 Methylomonas methanica (A1353_04640, OAI09603) 7 3 Methylomonas koyamae (A1356_04765, OAI29429) Methylogaea oryzae JCM 16910 (Ga0128369_1122, 2677968525) 9 0 Proteobacteria bacterium ST_bin16 (OQW81150) 100 100 Nitrosomonas sp. Nm120 (Ga0180021_11, 2727726885) 100 Nitrosomonas oligotropha Nm76 (Ga0105876_127, 2671671299) Proteobacteria bacterium SG_bin4 (OQW42842) Nitrosomonas sp. Is79A3 (NC_015731, 651002515) Nitrosomonas sp. Is79A3 (NC_015731, 651003225) 100 Nitrosolobus multiformis Nl4 (Ga0111718_121, 2671445702) 9 9 Nitrosolobus multiformis Nl13 (Ga0111715_135, 2671657233) 6 1 Nitrosospira sp. 56-18 (OJY08912) 100 Nitrosomonas sp. Nm34 (Ga0111714_1037, 2676386204) 5 4 Nitrosospira sp. APG3 (Ga0081662_178, 2636913632) Nitrosospira briensis C-128 (F822DRAFT_unitig_0_quiver_dupTrim_8202.1, 2588205070) 9 0 5 4 100 Nitrosospira sp. APG3 (Ga0081662_135, 2636912291) Crenothrix polyspora (SJM94235) Methylosarcina fibrata AML-C10 (A3OWDRAFT_scaffold1.1, 2517553761) Methylocaldum sp. 175 (JC06DRAFT_unitig_0_quiver.5, 2595102826) 7 4 Composite genome from Trout Bog Hypolimnion pan-assembly TBhypo.metabat.1380 (TH1380DRAFT_TH01379_TBL_comb47_HYPODRAFT_10003490.45, 2595262768) 100 Composite genome from Trout Bog Hypolimnion pan-assembly TBhypo.metabat.3552 (TH3552DRAFT_TBhypo_metabat_3552_10000949.11, 2582978841) Composite genome from Trout Bog Epilimnion pan-assembly TBepi.metabat.8031 (TE8031DRAFT_TBepi_metabat_8031_1014794.75, 2582897580) 100 Bradyrhizobium sp. LTSP885 (052833050) Bradyrhizobium sp. LTSPM299 (044591466) 8 2 Opitutus sp. GAS368 (Ga0132005_11, 2690566818) 100 Composite genome from Trout Bog Epilimnion pan-assembly TBepi.metabat.1800.v2 (TE01800DRAFT_TE01800_TBL_comb48_EPIDRAFT_1001966.59, 2595260104) Opitutae-129 (UID2982) (Ga0081615_1077, 2634852957) 5 1 Opitutus sp. GAS368 (Ga0132005_11, 2690565850) Tistlia consotaensis USBA 355 (Ga0111602_103, 2667905805) 4 6 Acidiphilium rubrum ATCC 35905 (Ga0104712_113, 2681880531) 100 Acidiphilium multivorum AIU301 (Apmu_0755_41, GAN75770) 100 Acidiphilium cryptum (081432845) 100 Acidocella facilis ATCC 35904 (T331DRAFT_scaffold00002.2, 2558109243) Acidocella sp. MX-AZ02 (AMPS01000188, 2534529065) 100 Acidocella aminolytica DSM 11237 (EJ11DRAFT_scaffold00022.22, 2585097958) 7 6 Burkholderia territorii (059807244) Burkholderia diffusa (059467121) 6 8 Burkholderia contaminans (071334897) Burkholderia lata (AOJ37486) 6 1Burkholderia pseudomultivorans (059482638) 4 1 Burkholderia cenocepacia DDS 22E-1 (Ga0059203_gi685643920.1, 2598452010) Burkholderia pseudomultivorans (AOI91739) Aquamicrobium sp. SK-2 (Ga0098313_1029, 2648568615) Burkholderia ubonensis (KVV32910) Cluster 2 9 7 Burkholderia ubonensis (059759890) 6 5 Burkholderia stabilis (GAU02319) Burkholderia cepacia (053077704) Pseudomonas mesoacidophila (084904304) 8 0 Burkholderia ubonensis (080408032) 8 5 Burkholderia ubonensis (KVP23108) Burkholderia pyrrocinia CH-67 (B392DRAFT_ALWI01000033_1.33, 2552801158) 9 4 Paraburkholderia nodosa (083245405) 9 5 Burkholderia nodosa DSM 21604 (A3CWDRAFT_scaffold_29.30, 2516023047) 9 8 Paraburkholderia mimosarum (051391183) 100 Burkholderia mimosarum NBRC 106338 (Ga0056710_1022, 2600793029) Burkholderia aspalathi LMG 27731 (Ga0075240_1003, 2671593425) 9 9 Paraburkholderia ginsengiterrae (OAJ53554) 100 Ferrovum sp.
Load more

Recommended publications
  • CUED Phd and Mphil Thesis Classes
    High-throughput Experimental and Computational Studies of Bacterial Evolution Lars Barquist Queens' College University of Cambridge A thesis submitted for the degree of Doctor of Philosophy 23 August 2013 Arrakis teaches the attitude of the knife { chopping off what's incomplete and saying: \Now it's complete because it's ended here." Collected Sayings of Muad'dib Declaration High-throughput Experimental and Computational Studies of Bacterial Evolution The work presented in this dissertation was carried out at the Wellcome Trust Sanger Institute between October 2009 and August 2013. This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This dissertation does not exceed the limit of 60,000 words as specified by the Faculty of Biology Degree Committee. This dissertation has been typeset in 12pt Computer Modern font using LATEX according to the specifications set by the Board of Graduate Studies and the Faculty of Biology Degree Committee. No part of this dissertation or anything substantially similar has been or is being submitted for any other qualification at any other university. Acknowledgements I have been tremendously fortunate to spend the past four years on the Wellcome Trust Genome Campus at the Sanger Institute and the European Bioinformatics Institute. I would like to thank foremost my main collaborators on the studies described in this thesis: Paul Gardner and Gemma Langridge. Their contributions and support have been invaluable. I would also like to thank my supervisor, Alex Bateman, for giving me the freedom to pursue a wide range of projects during my time in his group and for advice.
    [Show full text]
  • Candidatus Xiphinematincola Pachtaicus' Gen
    TAXONOMIC DESCRIPTION Palomares- Rius et al., Int. J. Syst. Evol. Microbiol. 2021;71:004888 DOI 10.1099/ijsem.0.004888 OPEN ACCESS ‘Candidatus Xiphinematincola pachtaicus' gen. nov., sp. nov., an endosymbiotic bacterium associated with nematode species of the genus Xiphinema (Nematoda, Longidoridae) Juan E. Palomares- Rius1,*, Carlos Gutiérrez- Gutiérrez2, Manuel Mota2, Wim Bert3, Myriam Claeys3, Vladimir V. Yushin4, Natalia E. Suzina5, Elena V. Ariskina5, Lyudmila I. Evtushenko5, Sergei A. Subbotin6,7 and Pablo Castillo1 Abstract An intracellular bacterium, strain IAST, was observed to infect several species of the plant- parasitic nematode genus Xiphin- ema (Xiphinema astaregiense, Xiphinema incertum, Xiphinema madeirense, Xiphinema pachtaicum, Xiphinema parapachydermum and Xiphinema vallense). The bacterium could not be recovered on axenic medium. The 16S rRNA gene sequence of IAST was found to be new, being related to the family Burkholderiaceae, class Betaproteobacteria. Fungal endosymbionts Mycoavidus cysteinexigens B1- EBT (92.9 % sequence identity) and ‘Candidatus Glomeribacter gigasporarum’ BEG34 (89.8 % identity) are the closest taxa and form a separate phylogenetic clade inside Burkholderiaceae. Other genes (atpD, lepA and recA) also separated this species from its closest relatives using a multilocus sequence analysis approach. These genes were obtained using a partial genome of this bacterium. The localization of the bacterium (via light and fluorescence in situ hybridization microscopy) is in the X. pachtaicum females clustered around the developing oocytes, primarily found embedded inside the epithelial wall cells of the ovaries, from where they are dispersed in the intestine. Transmission electron microscopy (TEM) observations sup- ported the presence of bacteria inside the nematode body, where they occupy ovaries and occur inside the intestinal epithelium.
    [Show full text]
  • Whole Genome Analyses Suggests That Burkholderia Sensu Lato Contains Two Additional Novel Genera (Mycetohabitans Gen
    G C A T T A C G G C A T genes Article Whole Genome Analyses Suggests that Burkholderia sensu lato Contains Two Additional Novel Genera (Mycetohabitans gen. nov., and Trinickia gen. nov.): Implications for the Evolution of Diazotrophy and Nodulation in the Burkholderiaceae Paulina Estrada-de los Santos 1,*,† ID , Marike Palmer 2,†, Belén Chávez-Ramírez 1, Chrizelle Beukes 2, Emma T. Steenkamp 2, Leah Briscoe 3, Noor Khan 3 ID , Marta Maluk 4, Marcel Lafos 4, Ethan Humm 3, Monique Arrabit 3, Matthew Crook 5, Eduardo Gross 6 ID , Marcelo F. Simon 7,Fábio Bueno dos Reis Junior 8, William B. Whitman 9, Nicole Shapiro 10, Philip S. Poole 11, Ann M. Hirsch 3,* ID , Stephanus N. Venter 2,* ID and Euan K. James 4,* ID 1 Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, 11340 Cd. de Mexico, Mexico; [email protected] 2 Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0083, South Africa; [email protected] (M.P.); [email protected] (C.B.); [email protected] (E.T.S.) 3 Department of Molecular, Cell, and Developmental Biology and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA; [email protected] (L.B.); [email protected] (N.K.); [email protected] (E.H.); [email protected] (M.A.) 4 The James Hutton Institute, Dundee DD2 5DA, UK; [email protected] (M.M.); [email protected] (M.L.) 5 450G Tracy Hall Science Building, Weber State University, Ogden, 84403 UT, USA; [email protected]
    [Show full text]
  • Phylogenetic Diversity of NTT Nucleotide Transport Proteins in Free-Living and Parasitic Bacteria and Eukaryotes
    Major, P., Embley, T. M., & Williams, T. (2017). Phylogenetic Diversity of NTT Nucleotide Transport Proteins in Free-Living and Parasitic Bacteria and Eukaryotes. Genome Biology and Evolution, 9(2), 480- 487. [evx015]. https://doi.org/10.1093/gbe/evx015 Publisher's PDF, also known as Version of record License (if available): CC BY Link to published version (if available): 10.1093/gbe/evx015 Link to publication record in Explore Bristol Research PDF-document This is the final published version of the article (version of record). It first appeared online via Oxford University Press at https://academic.oup.com/gbe/article/2970297/Phylogenetic. Please refer to any applicable terms of use of the publisher. University of Bristol - Explore Bristol Research General rights This document is made available in accordance with publisher policies. Please cite only the published version using the reference above. Full terms of use are available: http://www.bristol.ac.uk/red/research-policy/pure/user-guides/ebr-terms/ GBE Phylogenetic Diversity of NTT Nucleotide Transport Proteins in Free-Living and Parasitic Bacteria and Eukaryotes Peter Major1,T.MartinEmbley1, and Tom A. Williams2,* 1Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom 2School of Earth Sciences, University of Bristol, United Kingdom *Corresponding author: E-mail: [email protected]. Accepted: January 30, 2017 Abstract Plasma membrane-located nucleotide transport proteins (NTTs) underpin the lifestyle of important obligate intracellular bacterial and eukaryotic pathogens by importing energy and nucleotides from infected host cells that the pathogens can no longer make for themselves. As such their presence is often seen as a hallmark of an intracellular lifestyle associated with reductive genome evolution and loss of primary biosynthetic pathways.
    [Show full text]
  • Specificity in Legume-Rhizobia Symbioses
    International Journal of Molecular Sciences Review Specificity in Legume-Rhizobia Symbioses Mitchell Andrews * and Morag E. Andrews Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand; [email protected] * Correspondence: [email protected]; Tel.: +64-3-423-0692 Academic Editors: Peter M. Gresshoff and Brett Ferguson Received: 12 February 2017; Accepted: 21 March 2017; Published: 26 March 2017 Abstract: Most species in the Leguminosae (legume family) can fix atmospheric nitrogen (N2) via symbiotic bacteria (rhizobia) in root nodules. Here, the literature on legume-rhizobia symbioses in field soils was reviewed and genotypically characterised rhizobia related to the taxonomy of the legumes from which they were isolated. The Leguminosae was divided into three sub-families, the Caesalpinioideae, Mimosoideae and Papilionoideae. Bradyrhizobium spp. were the exclusive rhizobial symbionts of species in the Caesalpinioideae, but data are limited. Generally, a range of rhizobia genera nodulated legume species across the two Mimosoideae tribes Ingeae and Mimoseae, but Mimosa spp. show specificity towards Burkholderia in central and southern Brazil, Rhizobium/Ensifer in central Mexico and Cupriavidus in southern Uruguay. These specific symbioses are likely to be at least in part related to the relative occurrence of the potential symbionts in soils of the different regions. Generally, Papilionoideae species were promiscuous in relation to rhizobial symbionts, but specificity for rhizobial genus appears to hold at the tribe level for the Fabeae (Rhizobium), the genus level for Cytisus (Bradyrhizobium), Lupinus (Bradyrhizobium) and the New Zealand native Sophora spp. (Mesorhizobium) and species level for Cicer arietinum (Mesorhizobium), Listia bainesii (Methylobacterium) and Listia angolensis (Microvirga).
    [Show full text]
  • 1 Microbial Transformations of Organic Chemicals in Produced Fluid From
    Microbial transformations of organic chemicals in produced fluid from hydraulically fractured natural-gas wells Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Morgan V. Evans Graduate Program in Environmental Science The Ohio State University 2019 Dissertation Committee Professor Paula Mouser, Advisor Professor Gil Bohrer, Co-Advisor Professor Matthew Sullivan, Member Professor Ilham El-Monier, Member Professor Natalie Hull, Member 1 Copyrighted by Morgan Volker Evans 2019 2 Abstract Hydraulic fracturing and horizontal drilling technologies have greatly improved the production of oil and natural-gas from previously inaccessible non-permeable rock formations. Fluids comprised of water, chemicals, and proppant (e.g., sand) are injected at high pressures during hydraulic fracturing, and these fluids mix with formation porewaters and return to the surface with the hydrocarbon resource. Despite the addition of biocides during operations and the brine-level salinities of the formation porewaters, microorganisms have been identified in input, flowback (days to weeks after hydraulic fracturing occurs), and produced fluids (months to years after hydraulic fracturing occurs). Microorganisms in the hydraulically fractured system may have deleterious effects on well infrastructure and hydrocarbon recovery efficiency. The reduction of oxidized sulfur compounds (e.g., sulfate, thiosulfate) to sulfide has been associated with both well corrosion and souring of natural-gas, and proliferation of microorganisms during operations may lead to biomass clogging of the newly created fractures in the shale formation culminating in reduced hydrocarbon recovery. Consequently, it is important to elucidate microbial metabolisms in the hydraulically fractured ecosystem.
    [Show full text]
  • Yu-Chen Ling and John W. Moreau
    Microbial Distribution and Activity in a Coastal Acid Sulfate Soil System Introduction: Bioremediation in Yu-Chen Ling and John W. Moreau coastal acid sulfate soil systems Method A Coastal acid sulfate soil (CASS) systems were School of Earth Sciences, University of Melbourne, Melbourne, VIC 3010, Australia formed when people drained the coastal area Microbial distribution controlled by environmental parameters Microbial activity showed two patterns exposing the soil to the air. Drainage makes iron Microbial structures can be grouped into three zones based on the highest similarity between samples (Fig. 4). Abundant populations, such as Deltaproteobacteria, kept constant activity across tidal cycling, whereas rare sulfides oxidize and release acidity to the These three zones were consistent with their geological background (Fig. 5). Zone 1: Organic horizon, had the populations changed activity response to environmental variations. Activity = cDNA/DNA environment, low pH pore water further dissolved lowest pH value. Zone 2: surface tidal zone, was influenced the most by tidal activity. Zone 3: Sulfuric zone, Abundant populations: the heavy metals. The acidity and toxic metals then Method A Deltaproteobacteria Deltaproteobacteria this area got neutralized the most. contaminate coastal and nearby ecosystems and Method B 1.5 cause environmental problems, such as fish kills, 1.5 decreased rice yields, release of greenhouse gases, Chloroflexi and construction damage. In Australia, there is Gammaproteobacteria Gammaproteobacteria about a $10 billion “legacy” from acid sulfate soils, Chloroflexi even though Australia is only occupied by around 1.0 1.0 Cyanobacteria,@ Acidobacteria Acidobacteria Alphaproteobacteria 18% of the global acid sulfate soils. Chloroplast Zetaproteobacteria Rare populations: Alphaproteobacteria Method A log(RNA(%)+1) Zetaproteobacteria log(RNA(%)+1) Method C Method B 0.5 0.5 Cyanobacteria,@ Bacteroidetes Chloroplast Firmicutes Firmicutes Bacteroidetes Planctomycetes Planctomycetes Ac8nobacteria Fig.
    [Show full text]
  • Differential Depth Distribution of Microbial Function and Putative Symbionts Through Sediment-Hosted Aquifers in the Deep Terrestrial Subsurface
    ARTICLES https://doi.org/10.1038/s41564-017-0098-y Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface Alexander J. Probst1,5,7, Bethany Ladd2,7, Jessica K. Jarett3, David E. Geller-McGrath1, Christian M. K. Sieber1,3, Joanne B. Emerson1,6, Karthik Anantharaman1, Brian C. Thomas1, Rex R. Malmstrom3, Michaela Stieglmeier4, Andreas Klingl4, Tanja Woyke 3, M. Cathryn Ryan 2* and Jillian F. Banfield 1* An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome- resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus “Altiarchaeum sp.” and phylogenetically deep- branching nanoarchaea dominate the deepest groundwater. A nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. “Altiarchaeum”. Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface.
    [Show full text]
  • Revealing the Full Biosphere Structure and Versatile Metabolic Functions In
    Chen et al. Genome Biology (2021) 22:207 https://doi.org/10.1186/s13059-021-02408-w RESEARCH Open Access Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep Ping Chen1†, Hui Zhou1,2†, Yanyan Huang3,4†, Zhe Xie5†, Mengjie Zhang1,2†, Yuli Wei5, Jia Li1,2, Yuewei Ma3, Min Luo5, Wenmian Ding3, Junwei Cao5, Tao Jiang1,2, Peng Nan3*, Jiasong Fang5* and Xuan Li1,2* * Correspondence: nanpeng@fudan. edu.cn; [email protected]; lixuan@ Abstract sippe.ac.cn †Ping Chen, Hui Zhou, Yanyan Background: The full biosphere structure and functional exploration of the microbial Huang, Zhe Xie and Mengjie Zhang communities of the Challenger Deep of the Mariana Trench, the deepest known contributed equally to this work. hadal zone on Earth, lag far behind that of other marine realms. 3Ministry of Education Key Laboratory for Biodiversity Science Results: We adopt a deep metagenomics approach to investigate the microbiome and Ecological Engineering, School in the sediment of Challenger Deep, Mariana Trench. We construct 178 of Life Sciences, Fudan University, Shanghai, China metagenome-assembled genomes (MAGs) representing 26 phyla, 16 of which are 5Shanghai Engineering Research reported from hadal sediment for the first time. Based on the MAGs, we find the Center of Hadal Science and microbial community functions are marked by enrichment and prevalence of Technology, College of Marine Sciences, Shanghai Ocean mixotrophy and facultative anaerobic metabolism. The microeukaryotic community is University, Shanghai, China found to be dominated by six fungal groups that are characterized for the first time 1CAS-Key Laboratory of Synthetic in hadal sediment to possess the assimilatory and dissimilatory nitrate/sulfate Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute reduction, and hydrogen sulfide oxidation pathways.
    [Show full text]
  • Metabolic Versatility of the Nitrite-Oxidizing Bacterium Nitrospira
    bioRxiv preprint doi: https://doi.org/10.1101/2020.07.02.185504; this version posted July 4, 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 4.0 International license. 1 Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira 2 marina and its proteomic response to oxygen-limited conditions 3 Barbara Bayer1*, Mak A. Saito2, Matthew R. McIlvin2, Sebastian Lücker3, Dawn M. Moran2, 4 Thomas S. Lankiewicz1, Christopher L. Dupont4, and Alyson E. Santoro1* 5 6 1 Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, 7 CA, USA 8 2 Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, 9 Woods Hole, MA, USA 10 3 Department of Microbiology, IWWR, Radboud University, Nijmegen, The Netherlands 11 4 J. Craig Venter Institute, La Jolla, CA, USA 12 13 *Correspondence: 14 Barbara Bayer, Department of Ecology, Evolution and Marine Biology, University of California, 15 Santa Barbara, CA, USA. E-mail: [email protected] 16 Alyson E. Santoro, Department of Ecology, Evolution and Marine Biology, University of 17 California, Santa Barbara, CA, USA. E-mail: [email protected] 18 19 Running title: Genome and proteome of Nitrospira marina 20 21 Competing Interests: The authors declare that they have no conflict of interest. 22 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.02.185504; this version posted July 4, 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.
    [Show full text]
  • Microbiology of Seamounts Is Still in Its Infancy
    or collective redistirbution of any portion of this article by photocopy machine, reposting, or other means is permitted only with the approval of The approval portionthe ofwith any articlepermitted only photocopy by is of machine, reposting, this means or collective or other redistirbution This article has This been published in MOUNTAINS IN THE SEA Oceanography MICROBIOLOGY journal of The 23, Number 1, a quarterly , Volume OF SEAMOUNTS Common Patterns Observed in Community Structure O ceanography ceanography S BY DAVID EmERSON AND CRAIG L. MOYER ociety. © 2010 by The 2010 by O ceanography ceanography O ceanography ceanography ABSTRACT. Much interest has been generated by the discoveries of biodiversity InTRODUCTION S ociety. ociety. associated with seamounts. The volcanically active portion of these undersea Microbial life is remarkable for its resil- A mountains hosts a remarkably diverse range of unusual microbial habitats, from ience to extremes of temperature, pH, article for use and research. this copy in teaching to granted ll rights reserved. is Permission S ociety. ociety. black smokers rich in sulfur to cooler, diffuse, iron-rich hydrothermal vents. As and pressure, as well its ability to persist S such, seamounts potentially represent hotspots of microbial diversity, yet our and thrive using an amazing number or Th e [email protected] to: correspondence all end understanding of the microbiology of seamounts is still in its infancy. Here, we of organic or inorganic food sources. discuss recent work on the detection of seamount microbial communities and the Nowhere are these traits more evident observation that specific community groups may be indicative of specific geochemical than in the deep ocean.
    [Show full text]
  • (Antarctica) Glacial, Basal, and Accretion Ice
    CHARACTERIZATION OF ORGANISMS IN VOSTOK (ANTARCTICA) GLACIAL, BASAL, AND ACCRETION ICE Colby J. Gura A Thesis Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE December 2019 Committee: Scott O. Rogers, Advisor Helen Michaels Paul Morris © 2019 Colby Gura All Rights Reserved iii ABSTRACT Scott O. Rogers, Advisor Chapter 1: Lake Vostok is named for the nearby Vostok Station located at 78°28’S, 106°48’E and at an elevation of 3,488 m. The lake is covered by a glacier that is approximately 4 km thick and comprised of 4 different types of ice: meteoric, basal, type 1 accretion ice, and type 2 accretion ice. Six samples were derived from the glacial, basal, and accretion ice of the 5G ice core (depths of 2,149 m; 3,501 m; 3,520 m; 3,540 m; 3,569 m; and 3,585 m) and prepared through several processes. The RNA and DNA were extracted from ultracentrifugally concentrated meltwater samples. From the extracted RNA, cDNA was synthesized so the samples could be further manipulated. Both the cDNA and the DNA were amplified through polymerase chain reaction. Ion Torrent primers were attached to the DNA and cDNA and then prepared to be sequenced. Following sequencing the sequences were analyzed using BLAST. Python and Biopython were then used to collect more data and organize the data for manual curation and analysis. Chapter 2: As a result of the glacier and its geographic location, Lake Vostok is an extreme and unique environment that is often compared to Jupiter’s ice-covered moon, Europa.
    [Show full text]