High quality draft genome sequence of Meganema perideroedes str. Gr1T and a proposal for its reclassification to the family Meganemaceae fam. nov

Standards in Genomic Sciences

Volumn 10, Issue FEBRUARY2015, 2015, Pages

  McIlroy, Simon J ^a   Lapidus, Alla ^b,c   Thomsen, Trine R ^a   Han, James ^d   Haynes, Matthew ^d   Lobos, Elizabeth ^d   Huntemann, Marcel ^d   Pati, Amrita ^d   Ivanova, Natalia N ^d   Markowitz, Victor ^e   Verbarg, Susanne ^f   Woyke, Tanja ^d   Klenk, Hans Peter ^g   Kyrpides, Nikos ^d,h   Nielsen, Per H ^a  

^a AALBORG UNIVERSITY   (Denmark)

^b ST PETERSBURG STATE UNIVERSITY   (Russian Federation)

^c ST PETERSBURG ACADEMIC UNIVERSITY   (Russian Federation)

^d DOE JOINT GENOME INSTITUTE   (United States)

^e LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^f LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^g NEWCASTLE UNIVERSITY   (United Kingdom)

^h KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

Author keywords

Activated sludge; Bulking; Facultative methylotroph; Filamentous; Meganema; Meganemaceae; Wastewater

Indexed keywords

GENOMIC DNA; GLYCOGEN; METHANOL; POLYPHOSPHATE; RNA 16S;

ACTIVATED SLUDGE; ALPHAPROTEOBACTERIA; ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; DENITRIFICATION; DNA BASE COMPOSITION; FUNCTIONAL GENOMICS; GENE SEQUENCE; GENETIC SIMILARITY; GENOME SIZE; GENOTYPE PHENOTYPE CORRELATION; MAXIMUM LIKELIHOOD METHOD; MEGANEMA PERIDEROEDES; NONHUMAN; OXIDATION; SEQUENCE ANALYSIS;

EID: 84940509986     PISSN: None     EISSN: 19443277     Source Type: Journal    
DOI: 10.1186/s40793-015-0013-1     Document Type: Article

References (46)

1. Thomsen TR, Blackall LL, de Muro M, Nielsen JL, Nielsen PH. Meganema perideroedes gen. nov., sp. nov., a filamentous alphaproteobacterium from activated sludge. Int J Syst Evol Microbiol. 2006; 56:1865-68
2. Levantesi C, Beimfohr C, Geurkink B, Rossetti S, Thelen K, Krooneman J, Snaidr J, van der Waarde J, Tandoi V. Filamentous Alphaproteobacteria associated with bulking in industrial wastewater treatment plants. Syst Appl Microbiol. 2004; 27:716-27
3. Dionisi D, Beccari M, Di Gregorio S, Majone M, Papini MP, Vallini G. Storage of biodegradable polymers by an enriched microbial community in a sequencing batch reactor operated at high organic load rate. J Chem Technol Biotechnol. 2005; 80:1306-18
4. Dionisi D, Majone M, Vallini G, Di Gregorio S, Beccari M. Effect of the applied organic load rate on biodegradable polymer production by mixed microbial cultures in a sequencing batch reactor. Biotechnol Bioeng. 2006; 93:76-88
5. Majone M, Beccari M, Di Gregorio S, Dionisi D, Vallini G. Enrichment of activated sludge in a sequencing batch reactor for polyhydroxyalkanoate production. Water Sci Technol. 2006; 54(1):119-28
6. Beccari M, Bertin L, Dionisi D, Fava F, Lampis S, Majone M, Valentino F, Vallini G, Villano V. Exploiting olive oil mill effluents as a renewable resource for production of biodegradable polymers through a combined anaerobic-aerobic process. J Chem Technol Biotechnol. 2009; 84:901-08
7. Werker AG, Bengtsson SOH, Morgan-Sagastume F, Karlsson CAB, Blanchet EM. Method of treating wastewater and producing an activated sludge having a high biopolymer production potential. 2012. Patent No. US20120305478
8. Valentino F, Beccari M, Fraraccio S, Zanaroli G, Majone M. Feed frequency in a sequencing batch reactor strongly affects the production of polyhydroxyalkanoates (PHAs) from volatile fatty acids. N Biotechnol. 2014; 31:264-75
9. Kragelund C, Nielsen JL, Thomsen TR, Nielsen PH. Ecophysiology of the filamentous alphaproteobacterium Meganema perideroedes in activated sludge. FEMS Microbiol Ecol. 2005; 54:111-22
10. Yarza P, Ludwig W, Euzeby J, Amann R, Schleifer KH, Glockner FO, Rossello-Mora R. Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol. 2010; 33:291-99
11. Kelly DP, McDonald IR, Wood AP. Family Methylobacteriaceae. In: Rosenberg E, Delong EF, Lory S, Stackebrandt E, Thompson F, editors. The Prokaryotes-Alphaproteobacteria and Betaproteobacteria. Heidelberg: Springer-Verlag; 2014: p. 313-340
12. Garrity G, Bell J, Lilburn T. Family IX. Methylobacteriaceae fam. nov. In: Brenner D, Krieg N, Staley J, Garrity G, editors. Bergey’s Manual of Systematic Bacteriology Part C: The Alpha- Beta-, Delta-and Epsilonproteobacteria Vol 2. New York: Springer; 2005: p. 567-71
13. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar Buchner A, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüssmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, et al. ARB: a software environment for sequence data. Nucleic Acids Res. 2004; 32:1363-71
14. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Dawyndt P, Guralnick R, Goldstein P, Hall N, Hirschman L, Kravitz S, Lister AL, Markowitz V, Thomson N, Whetzel T. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008; 26:541-47
15. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the do-mains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990; 87:4576-79
16. Garrity GM, Bell JA, Lilburn T. Phylum XIV. Proteobacteria phyl. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM, editors. Bergey’s Manual of Systematic Bacteriology, 2nd edition, vol. 2 (The Proteobacteria), part B (The Gammaproteobacteria). New York: Springer; 2005: p. 1
17. Garrity GM, Bell JA, Lilburn T. Class I. Alphaproteobacteria class. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM, editors. Bergey’s Manual of Systematic Bacteriology, 2nd edition, vol. 2 (The Proteobacteria), part C (The Alpha-, Beta-, Delta-, and Epsilonproteobacteria). New York: Springer; 2005: p. 1
18. Kuykendall LD. Order VI. Rhizobiales ord. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM, editors. Bergey’s Manual of Systematic Bacteriology, 2nd edn, vol. 2 (The Proteobacteria), part C (The Alpha-,Beta-,Delta-, and Epsilonproteobacteria). New York: Springer; 2005: p. 324
19. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25:25-9
20. Klenk HP, Göker M. En route to a genome - based classification of Archaea and Bacteria? Syst Appl Microbiol. 2010; 33:175-82
21. Göker M, Klenk HP. Phylogeny-driven target selection for genome-sequencing (and other) projects. Stand Genomic Sci. 2013; 8:360-74
22. Kyrpides NC, Woyke T, Eisen JA, Garrity G, Lilburn TG, Beck BJ, Whitman WB, Hugenholz P, Klenk HP. Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project. Stand Genomic Sci. 2013; 9:628-34
23. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D’haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, et al. A phylogeny-driven Genomic Encyclopaedia of Bacteria and Archaea. Nature. 2009; 462:1056-60
24. Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC. The Genomes OnLine Database (GOLD) v. 4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2012; 40:D571-79
25. Mavromatis K, Land ML, Brettin TS, Quest DJ, Copeland A, Clum A, Goodwin L, Woyke T, Lapidus A, Klenk HP, Cottingham RE, Kyrpides NC. The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation. PLoS One. 2012; 7:e48837
26. List of growth media used at the DSMZ http://www.dmsz.de/catalogues/cataloque-microorganisms/culture-technology/list-of-media-for-microorganisms.html
27. Gemeinholzer B, Dröge G, Zetzsche H, Haszprunar G, Klenk HP, Güntsch AM, Berendsohn WG, Wägele JW. The DNA Bank Network: the start from a German initiative. Biopreserv Biobank. 2011; 9:51-5
28. Bennett S. Solexa Ltd. Pharmacogenomics. 2004; 5:433-38
29. JGI web site http://www.jgi.doe.gov
30. Zerbino D, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008; 18:821-29
31. Github https://github.com/lh3/wgsim
32. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiati on site identification. BMC Bioinformatics. 2010; 11:119
33. Mavromatis K, Ivanova NN, Chen IM, Szeto E, Markowitz VM, Kyrpides NC. The DOE-JGI Standard operating procedure for the annotations of microbial genomes. Stand Genomic Sci. 2009; 1:63-7
34. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods. 2010; 7:455-57
35. Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics. 2009; 25:2271-78
36. Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L, Lajus A, Rouy Z, Roche D, Salvignol G, Scarpelli C, Medigue C. MicroScope: a platform for microbial genome annotation and comparative genomics. Database (Oxford). 2009; 2009:bap021
37. Seviour RJ, Mino T, Onuki M. The microbiology of biological phosphorus removal in activated sludge systems. FEMS Microbiol Rev. 2003; 27:99-127
38. García Martín H, Ivanova N, Kunin V, Warnecke F, Barry KW, McHardy AC, Yeates C, He S, Salamov AA, Szeto E, Dalin E, Putnam NH, Shapiro HJ, Pangilinan JL, Rigoutsos I, Kyrpides NC, Blackall LL, McMahon KD, Hugenholtz P. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol. 2006; 24:1263-69
39. McIlroy SJ, Albertsen M, Andresen EK, Saunders AM, Kristiansen R, Stokholm-Bjerregaard M, Nielsen KL, Nielsen PH. “Candidatus Competibacter”- lineage genomes retrieved from metagenomes reveal functional metabolic diversity. ISME J. 2014; 8:613-24
40. Falvo A, Levantesi C, Rossetti S, Seviour R, Tandoi V. Synthesis of intracellular storage polymers by Amaricoccus kaplicensis, a tetrad forming bacterium present in activated sludge. J Appl Microbiol. 2001; 91:299-305
41. McIlroy SJ, Speirs LB, Tucci J, Seviour RJ. In situ profiling of microbial communities in full-scale aerobic sequencing batch reactors treating winery waste in Australia. Environ Sci Technol. 2011; 45:8794-803
42. McIlroy SJ. Phylogenetic diversity and ecophysiology of alphaproteobacterial glycogen accumulating organisms in enhanced biological phosphorus removal activated sludge systems. In: PhD Thesis. La Trobe University, School of Pharmacy and Applied Science; 2010
43. Lidstrom ME. Aerobic methylotrophic prokaryotes. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E, editors. The Prokaryotes, vol. 2 New York: Springer; 2006: p. 618-34
44. Anthony C. The Biochemistry of Methylotrophs. New York: Academic Press; 1982
45. Dedysh SN, Smirnova KV, Khmelenina VN, Suzina NE, Liesack W, Trotsenko YA. Methylotrophic autotrophy in Beijerinckia mobilis. J Bacteriol. 2005; 187:3884-88
46. Kindaichi T, Nierychlo M, Kragelund C, Nielsen JL, Nielsen PH. High and stable substrate specificities of microorganisms in enhanced biological phosphorus removal plants. Environ Microbiol. 2013; 15:1821-31