The Diversity and Metabolism of Culturable Nitrate-Reducing Bacteria from the Photic Zone of the Western North Pacific Ocean.
Diversity
Nitrate-reducing bacteria
Pacific Ocean
The photic zone
Journal
Microbial ecology
ISSN: 1432-184X
Titre abrégé: Microb Ecol
Pays: United States
ID NLM: 7500663
Informations de publication
Date de publication:
Nov 2023
Nov 2023
Historique:
received:
28
01
2023
accepted:
31
07
2023
medline:
13
11
2023
pubmed:
8
8
2023
entrez:
8
8
2023
Statut:
ppublish
Résumé
To better understand bacterial communities and metabolism under nitrogen deficiency, 154 seawater samples were obtained from 5 to 200 m at 22 stations in the photic zone of the Western North Pacific Ocean. Total 634 nitrate-utilizing bacteria were isolated using selective media and culture-dependent methods, and 295 of them were positive for nitrate reduction. These nitrate-reducing bacteria belonged to 19 genera and 29 species and among them, Qipengyuania flava, Roseibium aggregatum, Erythrobacter aureus, Vibrio campbellii, and Stappia indica were identified from all tested seawater layers of the photic zone and at almost all stations. Twenty-nine nitrate-reducing strains representing different species were selected for further the study of nitrogen, sulfur, and carbon metabolism. All 29 nitrate-reducing isolates contained genes encoding dissimilatory nitrate reduction or assimilatory nitrate reduction. Six nitrate-reducing isolates can oxidize thiosulfate based on genomic analysis and activity testing, indicating that nitrate-reducing thiosulfate-oxidizing bacteria exist in the photic zone. Five nitrate-reducing isolates obtained near the chlorophyll a-maximum layer contained a dimethylsulfoniopropionate synthesis gene and three of them contained both dimethylsulfoniopropionate synthesis and cleavage genes. This suggests that nitrate-reducing isolates may participate in dimethylsulfoniopropionate synthesis and catabolism in photic seawater. The presence of multiple genes for chitin degradation and extracellular peptidases may indicate that almost all nitrate-reducing isolates (28/29) can use chitin and proteinaceous compounds as important sources of carbon and nitrogen. Collectively, these results reveal culturable nitrate-reducing bacterial diversity and have implications for understanding the role of such strains in the ecology and biogeochemical cycles of nitrogen, sulfur, and carbon in the oligotrophic marine photic zone.
Identifiants
pubmed: 37552473
doi: 10.1007/s00248-023-02284-w
pii: 10.1007/s00248-023-02284-w
pmc: PMC10640468
doi:
Substances chimiques
dimethylpropiothetin
C884XA7QGG
Nitrates
0
Chlorophyll A
YF5Q9EJC8Y
Thiosulfates
0
Sulfur
70FD1KFU70
Nitrogen
N762921K75
Carbon
7440-44-0
Chitin
1398-61-4
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2781-2789Informations de copyright
© 2023. The Author(s).
Références
Nat Commun. 2020 Sep 16;11(1):4658
pubmed: 32938931
Nucleic Acids Res. 2014 Jan;42(Database issue):D503-9
pubmed: 24157837
ISME J. 2009 Dec;3(12):1374-86
pubmed: 19626056
Appl Environ Microbiol. 2009 May;75(10):3171-9
pubmed: 19304834
Appl Environ Microbiol. 2007 Sep;73(18):5971-4
pubmed: 17630306
Ann Rev Mar Sci. 2012;4:523-42
pubmed: 22457986
Biochem J. 2004 Sep 15;382(Pt 3):769-81
pubmed: 15214846
Nat Methods. 2015 Jan;12(1):59-60
pubmed: 25402007
Front Microbiol. 2018 Apr 25;9:797
pubmed: 29922238
Environ Microbiol. 2006 Dec;8(12):2083-95
pubmed: 17107550
Nat Microbiol. 2017 Feb 13;2:17009
pubmed: 28191900
Int J Syst Evol Microbiol. 2010 Nov;60(Pt 11):2618-2622
pubmed: 20023054
Sci Total Environ. 2012 Apr 1;421-422:184-96
pubmed: 22386232
FEMS Microbiol Ecol. 2014 Sep;89(3):580-93
pubmed: 24862403
Environ Sci Technol. 2016 Sep 20;50(18):9972-80
pubmed: 27499451
Appl Microbiol Biotechnol. 2006 Aug;71(6):773-82
pubmed: 16249876
J Microbiol. 2014 Oct;52(10):834-41
pubmed: 25269604
Mar Pollut Bull. 2022 Sep;182:113949
pubmed: 35932724
Genome Announc. 2018 May 17;6(20):
pubmed: 29773633
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
ISME J. 2014 Jul;8(7):1510-21
pubmed: 24430487
Mar Environ Res. 2008 Jun;65(5):445-55
pubmed: 18358526
J Microbiol Methods. 2020 Jan;168:105808
pubmed: 31837971
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
J Gen Appl Microbiol. 1998 Jun;44(3):201-210
pubmed: 12501429
Antonie Van Leeuwenhoek. 2010 Jun;98(1):9-18
pubmed: 20229220
FEMS Microbiol Lett. 2009 Sep;298(1):56-66
pubmed: 19659727
Mar Biotechnol (NY). 2011 Oct;13(5):823-30
pubmed: 21607543
Front Microbiol. 2012 Feb 27;3:45
pubmed: 22375137
Curr Protoc Bioinformatics. 2020 Jun;70(1):e102
pubmed: 32559359
Elife. 2021 May 10;10:
pubmed: 33970104
Proc Natl Acad Sci U S A. 2022 Sep 13;119(37):e2200014119
pubmed: 36067300
Appl Environ Microbiol. 2007 Feb;73(4):1266-76
pubmed: 17142374
3 Biotech. 2019 Nov;9(11):430
pubmed: 31696035
Mol Biol Evol. 2021 Sep 27;38(10):4647-4654
pubmed: 34320186
Appl Microbiol Biotechnol. 2017 Mar;101(5):2079-2092
pubmed: 27966049
Proc Natl Acad Sci U S A. 2009 Mar 24;106(12):4752-7
pubmed: 19255441
Int J Syst Evol Microbiol. 2003 Jul;53(Pt 4):1169-1174
pubmed: 12892146
Int J Syst Evol Microbiol. 2020 Dec;70(12):6257-6265
pubmed: 33095131
Annu Rev Microbiol. 2009;63:311-34
pubmed: 19575572
Mar Drugs. 2019 Jun 11;17(6):
pubmed: 31212714
Sci Rep. 2019 May 17;9(1):7546
pubmed: 31101870
PLoS One. 2012;7(6):e38749
pubmed: 22741028
Sci Total Environ. 2020 Dec 20;749:141682
pubmed: 33370886
Nucleic Acids Res. 2021 Jul 2;49(W1):W293-W296
pubmed: 33885785
J Biosci Bioeng. 2018 Mar;125(3):311-315
pubmed: 29100685
Sci Total Environ. 2021 Nov 15;795:148848
pubmed: 34246137
Microb Ecol. 2007 Nov;54(4):587-97
pubmed: 17851710
Sci Total Environ. 2021 Jun 10;772:145464
pubmed: 33571768
Nature. 2001 Jan 25;409(6819):507-10
pubmed: 11206545
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
Extremophiles. 2009 Jan;13(1):169-78
pubmed: 19050822
Science. 2010 Oct 8;330(6001):192-6
pubmed: 20929768
Sci China Life Sci. 2019 Oct;62(10):1296-1319
pubmed: 31231779
Appl Environ Microbiol. 2005 Dec;71(12):8958-62
pubmed: 16332899
Sci Rep. 2020 Apr 6;10(1):5949
pubmed: 32249806
Microbiol Mol Biol Rev. 1999 Mar;63(1):106-27
pubmed: 10066832
Nat Microbiol. 2019 Nov;4(11):1815-1825
pubmed: 31427729
Chem Soc Rev. 2014 Jan 21;43(2):676-706
pubmed: 24141308
Ann Rev Mar Sci. 2011;3:197-225
pubmed: 21329204
CEN Case Rep. 2021 Aug;10(3):402-408
pubmed: 33590472
Bioinformatics. 2014 Jul 15;30(14):2068-9
pubmed: 24642063
Nat Commun. 2018 Mar 2;9(1):915
pubmed: 29500422
mSystems. 2021 Aug 31;6(4):e0038321
pubmed: 34282940
Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314
pubmed: 30418610
Nucleic Acids Res. 2018 Jul 2;46(W1):W95-W101
pubmed: 29771380
J Bacteriol. 2011 Dec;193(23):6483-9
pubmed: 21949073
Appl Environ Microbiol. 2007 Jun;73(11):3612-22
pubmed: 17400770