دورية أكاديمية
أعرض في EDS

Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume.

التفاصيل البيبلوغرافية
العنوان: Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume.
المؤلفون: Pinto OHB; Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil., Silva TF; Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil., Vizzotto CS; Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil.; Department of Civil and Environmental Engineering, University of Brasília, Brasilia, 70910-900, Brazil., Santana RH; Federal Institute of Brasília, Brasilia, 70830-450, Brazil., Lopes FAC; Laboratory of Microbiology, Federal University of Tocantins, Palmas, 77500-000, Brazil., Silva BS; Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil., Thompson FL; Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil., Kruger RH; Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil. kruger@unb.br.
المصدر: BMC microbiology [BMC Microbiol] 2020 Jan 15; Vol. 20 (1), pp. 13. Date of Electronic Publication: 2020 Jan 15.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: BioMed Central Country of Publication: England NLM ID: 100966981 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2180 (Electronic) Linking ISSN: 14712180 NLM ISO Abbreviation: BMC Microbiol Subsets: MEDLINE
أسماء مطبوعة: Original Publication: London : BioMed Central, [2001-
مواضيع طبية MeSH: Genome, Archaeal*, Archaea/*classification , Rivers/*microbiology , Sequence Analysis, DNA/*methods, Archaea/genetics ; Archaea/isolation & purification ; Base Composition ; Genome Size ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Phylogeny
مستخلص: Background: Thaumarchaeota are abundant in the Amazon River, where they are the only ammonia-oxidizing archaea. Despite the importance of Thaumarchaeota, little is known about their physiology, mainly because few isolates are available for study. Therefore, information about Thaumarchaeota was obtained primarily from genomic studies. The aim of this study was to investigate the ecological roles of Thaumarchaeota in the Amazon River and the Amazon River plume.
Results: The archaeal community of the shallow in Amazon River and its plume is dominated by Thaumarchaeota lineages from group 1.1a, which are mainly affiliated to Candidatus Nitrosotenuis uzonensis, members of order Nitrosopumilales, Candidatus Nitrosoarchaeum, and Candidatus Nitrosopelagicus sp. While Thaumarchaeota sequences have decreased their relative abundance in the plume, Candidatus Nitrosopelagicus has increased. One genome was recovered from metagenomic data of the Amazon River (ThauR71 [1.05 Mpb]), and two from metagenomic data of the Amazon River plume (ThauP25 [0.94 Mpb] and ThauP41 [1.26 Mpb]). Phylogenetic analysis placed all three Amazon genome bins in Thaumarchaeota Group 1.1a. The annotation revealed that most genes are assigned to the COG subcategory coenzyme transport and metabolism. All three genomes contain genes involved in the hydroxypropionate/hydroxybutyrate cycle, glycolysis, tricarboxylic acid cycle, oxidative phosphorylation. However, ammonia-monooxygenase genes were detected only in ThauP41 and ThauR71. Glycoside hydrolases and auxiliary activities genes were detected only in ThauP25.
Conclusions: Our data indicate that Amazon River is a source of Thaumarchaeota, where these organisms are important for primary production, vitamin production, and nitrification.
References: Proc Natl Acad Sci U S A. 2010 May 11;107(19):8818-23. (PMID: 20421470)
Nucleic Acids Res. 2017 Jan 4;45(D1):D507-D516. (PMID: 27738135)
Nature. 2001 Jan 25;409(6819):507-10. (PMID: 11206545)
Int J Syst Evol Microbiol. 2018 Oct;68(10):3084-3095. (PMID: 30124400)
Nature. 2005 Jul 28;436(7050):538-41. (PMID: 16049484)
ISME J. 2015 Feb;9(2):461-71. (PMID: 25126756)
Methods Mol Biol. 2009;537:113-37. (PMID: 19378142)
Trends Microbiol. 2010 Aug;18(8):331-40. (PMID: 20598889)
Microb Ecol. 2008 Oct;56(3):420-6. (PMID: 18204798)
Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6513-8. (PMID: 19366673)
Elife. 2015 Mar 03;4:null. (PMID: 25735037)
Curr Opin Chem Biol. 2019 Apr;49:9-15. (PMID: 30236860)
Environ Microbiol. 2013 May;15(5):1647-58. (PMID: 22690844)
Environ Microbiol. 2008 Nov;10(11):3002-16. (PMID: 18973621)
FEMS Microbiol Ecol. 2010 Dec;74(3):566-74. (PMID: 21039653)
Science. 2012 Sep 28;337(6102):1661-5. (PMID: 23019650)
Proc Natl Acad Sci U S A. 2009 Apr 14;106(15):6333-8. (PMID: 19325122)
Nature. 2002 Apr 11;416(6881):617-20. (PMID: 11948346)
Nature. 2006 Aug 17;442(7104):806-9. (PMID: 16915287)
Environ Microbiol. 2005 Dec;7(12):1985-95. (PMID: 16309395)
Mol Biol Evol. 2013 Apr;30(4):772-80. (PMID: 23329690)
Mol Biol Evol. 2002 May;19(5):631-9. (PMID: 11961097)
Environ Microbiol. 2008 Mar;10(3):810-8. (PMID: 18205821)
Proc Natl Acad Sci U S A. 1992 Jun 15;89(12):5685-9. (PMID: 1608980)
Proc Natl Acad Sci U S A. 2006 Nov 28;103(48):18296-301. (PMID: 17114289)
Int J Syst Evol Microbiol. 2017 Dec;67(12):5067-5079. (PMID: 29034851)
Nucleic Acids Res. 2015 Aug 18;43(14):6761-71. (PMID: 26150420)
Nat Commun. 2018 Apr 17;9(1):1517. (PMID: 29666365)
Environ Microbiol. 2009 Jul;11(7):1658-71. (PMID: 19236445)
Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21206-11. (PMID: 22158986)
PLoS One. 2013;8(4):e61087. (PMID: 23565298)
Front Microbiol. 2013 Apr 09;4:72. (PMID: 23577005)
ISME J. 2008 Apr;2(4):429-41. (PMID: 18200070)
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W182-5. (PMID: 17526522)
Annu Rev Microbiol. 2012;66:83-101. (PMID: 22994489)
Proc Natl Acad Sci U S A. 2016 Dec 6;113(49):E7937-E7946. (PMID: 27864514)
ISME J. 2014 Mar;8(3):732-736. (PMID: 24196320)
Science. 1997 Oct 24;278(5338):631-7. (PMID: 9381173)
Curr Opin Microbiol. 2011 Jun;14(3):300-6. (PMID: 21546306)
Sci Adv. 2016 Apr 22;2(4):e1501252. (PMID: 27152336)
FEMS Microbiol Rev. 2009 Sep;33(5):855-69. (PMID: 19453522)
Nat Rev Microbiol. 2008 Mar;6(3):245-52. (PMID: 18274537)
PLoS Biol. 2006 Apr;4(4):e95. (PMID: 16533068)
Environ Microbiol. 2012 Dec;14(12):3122-45. (PMID: 23057602)
Environ Microbiol. 2007 May;9(5):1162-75. (PMID: 17472632)
Proc Natl Acad Sci U S A. 2014 Jul 29;111(30):11085-90. (PMID: 25024226)
Stand Genomic Sci. 2015 Oct 26;10:86. (PMID: 26512311)
BMC Microbiol. 2012 Dec 23;12:302. (PMID: 23259572)
Nature. 2008 Dec 11;456(7223):788-91. (PMID: 19037244)
Genome Biol Evol. 2014 Dec 19;7(1):191-204. (PMID: 25527841)
Nature. 2005 Sep 22;437(7058):543-6. (PMID: 16177789)
ISME J. 2016 Nov;10(11):2605-2619. (PMID: 27187795)
Bioinformatics. 2012 Jun 1;28(11):1420-8. (PMID: 22495754)
FEMS Microbiol Ecol. 2013 Feb;83(2):515-26. (PMID: 22984895)
Nature. 2009 Oct 15;461(7266):976-9. (PMID: 19794413)
Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):8239-44. (PMID: 24843170)
mSphere. 2017 Oct 4;2(5):null. (PMID: 28989970)
Microbes Environ. 2018 Dec 28;33(4):428-434. (PMID: 30318500)
Appl Environ Microbiol. 2015 Mar;81(5):1700-7. (PMID: 25548047)
Environ Microbiol. 2003 Sep;5(9):787-97. (PMID: 12919414)
Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12317-22. (PMID: 16894176)
Int J Syst Evol Microbiol. 2007 Jan;57(Pt 1):81-91. (PMID: 17220447)
Nat Methods. 2015 Jan;12(1):59-60. (PMID: 25402007)
Environ Sci Pollut Res Int. 2017 Sep;24(25):20409-20421. (PMID: 28707243)
Environ Microbiol. 2017 Feb;19(2):459-474. (PMID: 27112493)
Nat Rev Microbiol. 2005 Jun;3(6):479-88. (PMID: 15931166)
Proc Natl Acad Sci U S A. 2011 May 17;108(20):8420-5. (PMID: 21525411)
FEMS Microbiol Ecol. 2010 Jun;72(3):370-85. (PMID: 20402778)
ISME J. 2011 Nov;5(11):1796-808. (PMID: 21562601)
Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19126-31. (PMID: 19855009)
PLoS One. 2013 Nov 20;8(11):e80835. (PMID: 24278328)
Nat Protoc. 2009;4(4):470-83. (PMID: 19300441)
Proc Natl Acad Sci U S A. 2011 Oct 4;108(40):16771-6. (PMID: 21930919)
Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):15892-7. (PMID: 21896746)
PLoS One. 2012;7(6):e36687. (PMID: 22679480)
ISME J. 2015 Dec;9(12):2740-4. (PMID: 26000553)
Environ Microbiol. 2014 Mar;16(3):689-700. (PMID: 23848190)
ISME J. 2016 Jan;10(1):85-96. (PMID: 26140533)
Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14683-8. (PMID: 16186488)
ISME J. 2012 Feb;6(2):227-30. (PMID: 22071344)
Appl Environ Microbiol. 2000 May;66(5):1777-87. (PMID: 10788339)
Environ Microbiol. 2008 Jun;10(6):1601-11. (PMID: 18336563)
FEMS Microbiol Ecol. 2008 May;64(2):167-74. (PMID: 18355293)
Nucleic Acids Res. 2014 Jan;42(Database issue):D490-5. (PMID: 24270786)
معلومات مُعتمدة: 0 International Conselho Nacional de Desenvolvimento Científico e Tecnológico; 0 International Coordenação de Aperfeiçoamento de Pessoal de Nível Superior; 0 International Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro; 0 International Fundação de Apoio à Pesquisa do Distrito Federal
فهرسة مساهمة: Keywords: Amazon River; Amazon River plume; Metagenome-assembled genome; Thaumarchaeota
تواريخ الأحداث: Date Created: 20200117 Date Completed: 20210406 Latest Revision: 20210406
رمز التحديث: 20221213
مُعرف محوري في PubMed: PMC6964070
DOI: 10.1186/s12866-020-1698-x
PMID: 31941452
قاعدة البيانات: MEDLINE
الوصف
تدمد:1471-2180
DOI:10.1186/s12866-020-1698-x