Discovering the bacteriome of Vitis vinifera cv. Pinot Noir in a conventionally managed vineyard.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
15 04 2020
15 04 2020
Historique:
received:
15
01
2020
accepted:
16
03
2020
entrez:
17
4
2020
pubmed:
17
4
2020
medline:
15
12
2020
Statut:
epublish
Résumé
The structure of the bacteriome associated with grapevine roots can affect plant development, health and grape quality. We previously investigated the bacterial biodiversity of the Vitis vinifera cv. Pinot Noir rhizosphere in a vineyard subjected to integrated pest management. The aim of this work is to characterize the bacteriome of V. vinifera cv. Pinot Noir in a conventionally managed vineyard using a metabarcoding approach. Comparisons between the microbial community structure in bulk soil and rhizosphere (variable space) were performed and shifts of bacteriome according to two sampling times (variable time) were characterized. Bacterial biodiversity was higher at the second than at the first sampling and did not differ according to the variable space. Actinobacteria was the dominant class, with Gaiella as the most represented genus in all the samples. Among Proteobacteria, the most represented classes were Alpha, Beta and Gamma-Proteobacteria, with higher abundance at the second than at the first sampling time. Bradyrhizobium was the most frequent genus among Alpha-Proteobacteria, while Burkholderia was the predominant Beta-Proteobacteria. Among Firmicutes, the frequency of Staphylococcus was higher than 60% in bulk soil and rhizosphere. Finally, the sampling time can be considered as one of the drivers responsible for the bacteriome variations assessed.
Identifiants
pubmed: 32296119
doi: 10.1038/s41598-020-63154-w
pii: 10.1038/s41598-020-63154-w
pmc: PMC7160115
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
6453Commentaires et corrections
Type : ErratumIn
Références
Microbiome. 2018 Jan 3;6(1):3
pubmed: 29298729
BMC Microbiol. 2014 Jul 21;14:198
pubmed: 25048741
Nat Rev Microbiol. 2013 Nov;11(11):789-99
pubmed: 24056930
Antonie Van Leeuwenhoek. 2015 Feb;107(2):575-88
pubmed: 25527391
Front Plant Sci. 2016 May 23;7:711
pubmed: 27242887
FEMS Microbiol Rev. 2008 Aug;32(5):723-35
pubmed: 18549407
Antonie Van Leeuwenhoek. 2010 May;97(4):389-99
pubmed: 20352404
Can J Microbiol. 2001 Feb;47(2):110-7
pubmed: 11261489
Can J Microbiol. 2002 Sep;48(9):772-86
pubmed: 12455609
Microb Biotechnol. 2017 Mar;10(2):354-370
pubmed: 27778455
Syst Appl Microbiol. 2011 Dec;34(8):595-9
pubmed: 21899973
Environ Microbiol. 2015 Mar;17(3):610-21
pubmed: 24628845
Sci Total Environ. 2016 Feb 1;543(Pt A):155-160
pubmed: 26580738
BMC Plant Biol. 2016 Mar 21;16:67
pubmed: 27001212
PLoS One. 2014 Nov 11;9(11):e112763
pubmed: 25387008
BMC Plant Biol. 2014 Apr 17;14:99
pubmed: 24739459
New Phytol. 2015 Jun;206(4):1196-206
pubmed: 25655016
Microbes Infect. 2002 Apr;4(4):481-9
pubmed: 11932199
J Bacteriol. 1991 Jan;173(2):697-703
pubmed: 1987160
Appl Environ Microbiol. 2002 Jul;68(7):3328-38
pubmed: 12089011
Annu Rev Phytopathol. 2001;39:225-58
pubmed: 11701865
ISME J. 2014 Nov;8(11):2349-51
pubmed: 24824669
Microb Biotechnol. 2014 Nov;7(6):487-95
pubmed: 25186140
Antonie Van Leeuwenhoek. 2009 May;95(4):319-34
pubmed: 19247797
J Microbiol. 2012 Oct;50(5):754-65
pubmed: 23124742
Appl Environ Microbiol. 2007 Aug;73(16):5261-7
pubmed: 17586664
Front Microbiol. 2019 Jan 08;9:3203
pubmed: 30671035
Indian J Exp Biol. 2001 Dec;39(12):1318-21
pubmed: 12018534
Nat Commun. 2016 Jul 12;7:12151
pubmed: 27402057
PLoS One. 2013;8(2):e55731
pubmed: 23383346
Plant Signal Behav. 2009 Aug;4(8):777-80
pubmed: 19820328
Sci Total Environ. 2017 Jan 15;577:84-93
pubmed: 27817923
Plant Physiol Biochem. 2018 Jun;127:256-268
pubmed: 29627732
FEMS Microbiol Ecol. 2019 Jan 1;95(1):
pubmed: 30307579
Mol Biol Evol. 2014 May;31(5):1059-65
pubmed: 24554779
Trends Plant Sci. 2018 Jan;23(1):25-41
pubmed: 29050989
J Environ Sci Health B. 2010 Jul;45(5):348-59
pubmed: 20512724
FEMS Microbiol Ecol. 2014 May;88(2):424-35
pubmed: 24597529
Front Microbiol. 2014 Jul 08;5:327
pubmed: 25071740
Trends Plant Sci. 2012 Aug;17(8):478-86
pubmed: 22564542
PLoS One. 2009 Oct 09;4(10):e7401
pubmed: 19816594
Front Microbiol. 2019 May 22;10:1142
pubmed: 31178845
J Bacteriol. 2005 Nov;187(21):7292-308
pubmed: 16237012
BMC Evol Biol. 2010 Jun 03;10:164
pubmed: 20525265
FEMS Microbiol Ecol. 2003 May 1;44(2):203-15
pubmed: 19719637
FEMS Microbiol Ecol. 2003 Jun 1;44(3):335-46
pubmed: 12830827
Can J Microbiol. 2004 Apr;50(4):239-49
pubmed: 15213748
Curr Opin Biotechnol. 2014 Jun;27:15-20
pubmed: 24863892
J Sci Food Agric. 2015 Jan;95(1):193-203
pubmed: 24756770
Environ Microbiol. 2008 Apr;10(4):926-41
pubmed: 18218029
FEMS Microbiol Rev. 2017 Sep 1;41(5):599-623
pubmed: 28961933
Annu Rev Phytopathol. 2008;46:53-73
pubmed: 18680423
Genome Res. 1998 Mar;8(3):175-85
pubmed: 9521921
Molecules. 2014 Sep 02;19(9):13683-703
pubmed: 25185071
FEMS Microbiol Ecol. 2009 Apr;68(1):1-13
pubmed: 19243436
FEMS Microbiol Ecol. 2008 Aug;65(2):193-201
pubmed: 18616582
Sci Total Environ. 2018 May 15;624:294-308
pubmed: 29253777
Front Microbiol. 2017 Aug 14;8:1528
pubmed: 28855895
Nucleic Acids Res. 2017 Jul 3;45(W1):W180-W188
pubmed: 28449106
J Exp Bot. 2005 Jul;56(417):1761-78
pubmed: 15911555
Environ Microbiol. 2005 Nov;7(11):1673-85
pubmed: 16232283
New Phytol. 2006;170(1):165-75
pubmed: 16539613
Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):E139-48
pubmed: 24277822