IJSEM Papers in Press. Published May 18, 2015 as doi:10.1099/ijs.0.000339
International Journal of Systematic and Evolutionary Microbiology Novosphingobium gossypii sp. nov., isolated from Gossypium hirsutum --Manuscript Draft-Manuscript Number:
IJS-D-15-00049R1
Full Title:
Novosphingobium gossypii sp. nov., isolated from Gossypium hirsutum
Short Title:
Novosphingobium gossypii sp. nov.
Article Type:
Note
Section/Category:
New taxa - Proteobacteria
Corresponding Author:
Peter Kämpfer Justus-Liebig-Universität Giessen Giessen, GERMANY
First Author:
Peter Kämpfer
Order of Authors:
Peter Kämpfer Karin Martin John A. McInroy Stefanie P. Glaeser
Manuscript Region of Origin:
GERMANY
Abstract:
A gram-negative, rod-shaped, non-spore-forming bacterium (strain JM-1396T) producing a yellow pigment, was isolated from the healthy internal stem tissue of postharvest cotton (Gossypium hirsutum, cultivar 'DES-119') grown at the Plant Breeding Unit facility at the E.V. Smith Research Center in Tallassee (Macon county), Alabama USA. 16S rRNA gene sequence analysis of strain JM-1396T showed high sequence similarity values to the type strains of Novosphingobium mathurense, Novosphingobium panipatense (both 98.6%), and Novosphingobium barchaimii (98.5%); sequence similarities to all other Novosphingobium species type strains were below 98.3%. DNA-DNA pairing experiments of the DNA of strain JM-1396T and N. mathurense SM117T, N. panipatense SM16T and N. barchaimii DSM 25411T showed low similarity values of 8% (reciprocal: 7%), 24% (reciprocal 26%), and 19% (reciprocal 25%), respectively. Ubiquinone Q-10 was detected as the dominant quinone; the fatty acids C18:1 7c (71.0%) and the typical 2-hydroxy fatty acid, C14:0 2-OH (11.7%), were detected as typical components. The polar lipid profile contained the diagnostic lipids diphosphatidylglycerol, phosphatedylethanolamine, sphingoglycolipid and phosphatidylcholine. The polyamine pattern contained the major compound spermidine and only minor amounts of other polyamines. All these data revealed that strain JM-1396T represents a new species of the genus Novosphingobium. For this reason we propose the name Novosphingobium gossypii sp. nov. with the type strain JM-1396T (= LMG 28605T = CCM 8569T = CIP 110884T).
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1
Novosphingobium gossypii sp. nov., isolated from Gossypium
2
hirsutum
3 4
Peter Kämpfer1, Karin Martin2, John A. McInroy3, Stefanie P. Glaeser1
5
1
6
Germany
7
2
8
D-07745 Jena, Germany
9
3
Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen,
Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V., Hans-Knöll-Institut.,
Department of Entomology and Plant Pathology, Auburn University, Alabama, 36849 USA
10
Category: New Taxa -Proteobacteria
11
Running title: Novosphingobium gossypii sp. nov.
12
Key words: Novosphingobium, gossypii, taxonomy
13 14
Corresponding author:
15
Professor Dr. Peter Kämpfer
16
Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen
17
Heinrich-Buff-Ring 26–32; D-35392 Giessen, Germany
18
Tel. +49 641 99 37352 ; Fax. +49 641 99 37359
19
e-mail: [email protected]
20 21
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain JM-
22
1396T is KP657488.
1
1
Summary
2
A gram-negative, rod-shaped, non-spore-forming bacterium (strain JM-1396T) producing a
3
yellow pigment, was isolated from the healthy internal stem tissue of post-harvest cotton
4
(Gossypium hirsutum, cultivar ‘DES-119’) grown at the Plant Breeding Unit facility at the E.V.
5
Smith Research Center in Tallassee (Macon county), Alabama USA. 16S rRNA gene sequence
6
analysis of strain JM-1396T showed high sequence similarity values to the type strains of
7
Novosphingobium
8
Novosphingobium barchaimii (98.5%); sequence similarities to all other Novosphingobium
9
species type strains were below 98.3%. DNA-DNA pairing experiments of the DNA of strain
10
JM-1396T and N. mathurense SM117T, N. panipatense SM16T and N. barchaimii DSM 25411T
11
showed low similarity values of 8% (reciprocal: 7%), 24% (reciprocal 26%), and 19%
12
(reciprocal 25%), respectively.
13
Ubiquinone Q-10 was detected as the dominant quinone; the fatty acids C18:1 7c (71.0%) and
14
the typical 2-hydroxy fatty acid, C14:0 2-OH (11.7%), were detected as typical components. The
15
polar
16
phosphatedylethanolamine, sphingoglycolipid and phosphatidylcholine. The polyamine pattern
17
contained the major compound spermidine and only minor amounts of other polyamines.
18
All these data revealed that strain JM-1396T represents a new species of the genus
19
Novosphingobium. For this reason we propose the name Novosphingobium gossypii sp. nov.
20
with the type strain JM-1396T (= LMG 28605T = CCM 8569T = CIP 110884T).
lipid
mathurense,
profile
Novosphingobium
contained
the
panipatense
diagnostic
21
2
lipids
(both
98.6%),
and
diphosphatidylglycerol,
1
Representatives of the genus Novosphingobium were isolated from a large variety of
2
environmental sources including coastal and freshwater sediments and soil (Balkwill et al.,
3
1997; Sohn et al., 2004; Liu et al., 2005), surface water layers of lakes (Glaeser et al., 2009;
4
2013a, b), activated sludge/wastewater treatment plants (Neef et al., 1999; Fujii et al., 2003),
5
contaminated groundwater bioremediation reactor (Tiirola et al., 2002; 2005), and have also
6
been recently found associated with plants (Lin et al., 2014; Kämpfer et al., 2015). At the time
7
of writing 28 Novosphingobium species were described with validated names: N. acidiphilum
8
(Glaeser et al., 2009), N. aquaticum (Glaeser et al., 2013a), N. arabidopsis (Lin et al., 2014),
9
N. aromaticivorans (Balkwill et al., 1997), N. barchaimii (Niharika et al., 2013), N. capsulatum
10
(Yabuuchi et al., 1990), N. chloroacetimidivorans (Chen et al., 2014), N. fuchskuhlense
11
(Glaeser et al., 2013b), N. hassiacum (Kämpfer et al., 2002), N. indicum (Yuan et al., 2009),
12
N. kunmingense (Xie et al., 2014), N. lentum (Tiirola et al., 2005), N. lindaniclasticum (Saxena
13
et al., 2013), N. malaysiense (Lee et al., 2014a), N. mathurense and N. panipatense (Gupta et
14
al., 2009), N. naphthalenivorans (Suzuki & Hiraishi, 2007), N. nitrogenifigens (Addison et al.,
15
2007), N. pentaromativorans (Sohn et al., 2004), N. rosa (Takeuchi et al., 1995), N.
16
resinovorum (Lim et al., 2007), N. sediminicola (Baek et al., 2011), N. soli (Kämpfer et al.,
17
2011), N. stygium (Balkwill et al., 1997), N. subarcticum (which is a later subjective synonym
18
of N. resinivorum; Lim et al., 2007), N. subterraneum (Balkwill et al., 1997), N. taihuense (Liu
19
et al., 2005), and N. tardaugens (Fujii et al., 2003). Two further species proposals were recently
20
published, but the species names so far not validated, “N. ginsenosidimutans” (Kim et al., 2013)
21
and “N. aquiterrae” (Lee et al., 2014b).
22
Strain JM-1396T was isolated from the healthy internal stem tissue of post-harvest cotton
23
(Gossypium hirsutum, cultivar ‘DES-119’) grown at the Plant Breeding Unit facility at the E.V.
24
Smith Research Center in Tallassee (Macon county), Alabama USA. This isolate showed
25
microscopically single cells and formed small yellow colonies (70% are depicted. Nodes marked with circles were also conserved in the
7
maximum-parsimony tree, whereas larger circle were supported by a bootstrap value >70%.
8
Scale bar indicates 0.1 substitutions per 100 nucleotides.
9 10 11
Fig. 2.
12
Total polar lipid profile of strain JM-1396T after two-dimensional chromatography stained with
13
molybdatophosphoric acid. DPG, diphosphatidylglycerol; PE, phosphatidylethanolamine;
14
PDE, phosphatidyldimethylethanolamine; PG, phosphatidylglycerol, SGL, sphingoglycolipid,
15
PL1, PL2, unknown phospholipids, L1-L4, unknown lipids, AL1, unknown aminolipid, yPig,
16
yellow pigment.
17
19
Novosphingobium acidiphilum FSW06−204dT (EU336977) Novosphingobium nitrogenifigens Y88T (DQ448852) Novosphingobium taihuense T3−B9T (AY500142) T 98 Novosphingobium fuchskuhlense FNE08-7 (JN399172) T 87 Novosphingobium stygium IFO 16085 (AB025013) Novosphingobium sediminis YG−17T (FJ938155) Novosphingobium hassiacum W-51T (AJ416411) Novosphingobium lentum MT1T (AJ303009) Novosphingobium tardaugens ARI−1T (AB070237) Novosphingobium subterraneum IFO 16086T (AB025014) 98 Novosphingobium aquiterrae E−II−3T (FJ772064) Novosphingobium kunmingense 18−11HKT (JQ246446) Novosphingobium ginsenosidimutans FW−6T (JQ349046) Novosphingobium arabidopsis CC−ALB−2T (KC479803) Novosphingobium aromaticivorans DSM 12444T (CP000248) 99 Novosphingobium rhizosphaerae JM−1T (KM365125) Novosphingobium capsulatum GIFU11526T (D16147) Novosphingobium barchaimii LL02T (JN695619) Novosphingobium resinovorum NCIMB 8767T (EF029110) Novosphingobium lindaniclasticum LE124T (JN687581) Novosphingobium malaysiense MUSC 273T (KC907395) 94 Novosphingobium marinum LA53T (KJ708552) Novosphingobium indicum H25T (EF549586) 89 Novosphingobium mathurense SM117T (EF424403) Novosphingobium pentaromativorans US6−1T (AF502400) Novosphingobium gossypii JM−1396T (KP657488) Novosphingobium panipatense SM16T ( EF424402) Novosphingobium naphthalenivorans TUT562T (AB177883) Novosphingobium soli CC−TPE−1T (FJ425737) Novosphingobium chloroacetimidivorans BUT−14T (KF676669) Novosphingobium rosa IAM 14222T (D13945) Novosphingobium sediminicola HU1−AH51T (FJ177534) Novosphingobium aquaticum FNE08−86T (JN399173) 98 Sphingomicrobium astaxanthinifaciens CC−AMO−30BT (JX235675) 100 Sphingomicrobium lutaoense CC−TBT−3T (EU564841) 100 Sphingomicrobium marinum CC−AMZ−30MT (JX235672) Sphingomicrobium flavum CC−AMZ−30NT (JX393854)
Figure 1 100 Click here to download Figure: Fig-1.pdf
100
91
0.10
Figure 2 (NO BETTER RESOLUTION AVAILABLE) Click here to download Figure: Fig-2.docx
PL1
yPig L1 L2
DPG
PL2
PDE PG
SGL L3 AL1
L4
PE
International Journal of Systematic and Evolutionary Microbiology Novosphingobium gossypii sp. nov., isolated from Gossypium hirsutum --Manuscript Draft-Manuscript Number:
IJS-D-15-00049R1
Full Title:
Novosphingobium gossypii sp. nov., isolated from Gossypium hirsutum
Short Title:
Novosphingobium gossypii sp. nov.
Article Type:
Note
Section/Category:
New taxa - Proteobacteria
Corresponding Author:
Peter Kämpfer Justus-Liebig-Universität Giessen Giessen, GERMANY
First Author:
Peter Kämpfer
Order of Authors:
Peter Kämpfer Karin Martin John A. McInroy Stefanie P. Glaeser
Manuscript Region of Origin:
GERMANY
Abstract:
A gram-negative, rod-shaped, non-spore-forming bacterium (strain JM-1396T) producing a yellow pigment, was isolated from the healthy internal stem tissue of postharvest cotton (Gossypium hirsutum, cultivar 'DES-119') grown at the Plant Breeding Unit facility at the E.V. Smith Research Center in Tallassee (Macon county), Alabama USA. 16S rRNA gene sequence analysis of strain JM-1396T showed high sequence similarity values to the type strains of Novosphingobium mathurense, Novosphingobium panipatense (both 98.6%), and Novosphingobium barchaimii (98.5%); sequence similarities to all other Novosphingobium species type strains were below 98.3%. DNA-DNA pairing experiments of the DNA of strain JM-1396T and N. mathurense SM117T, N. panipatense SM16T and N. barchaimii DSM 25411T showed low similarity values of 8% (reciprocal: 7%), 24% (reciprocal 26%), and 19% (reciprocal 25%), respectively. Ubiquinone Q-10 was detected as the dominant quinone; the fatty acids C18:1 7c (71.0%) and the typical 2-hydroxy fatty acid, C14:0 2-OH (11.7%), were detected as typical components. The polar lipid profile contained the diagnostic lipids diphosphatidylglycerol, phosphatedylethanolamine, sphingoglycolipid and phosphatidylcholine. The polyamine pattern contained the major compound spermidine and only minor amounts of other polyamines. All these data revealed that strain JM-1396T represents a new species of the genus Novosphingobium. For this reason we propose the name Novosphingobium gossypii sp. nov. with the type strain JM-1396T (= LMG 28605T = CCM 8569T = CIP 110884T).
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Manuscript Including References (Word document) Click here to download Manuscript Including References (Word document): Novosphingobium_gossypii_manu5-with-tables-without-fig
1
Novosphingobium gossypii sp. nov., isolated from Gossypium
2
hirsutum
3 4
Peter Kämpfer1, Karin Martin2, John A. McInroy3, Stefanie P. Glaeser1
5
1
6
Germany
7
2
8
D-07745 Jena, Germany
9
3
Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen,
Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V., Hans-Knöll-Institut.,
Department of Entomology and Plant Pathology, Auburn University, Alabama, 36849 USA
10
Category: New Taxa -Proteobacteria
11
Running title: Novosphingobium gossypii sp. nov.
12
Key words: Novosphingobium, gossypii, taxonomy
13 14
Corresponding author:
15
Professor Dr. Peter Kämpfer
16
Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen
17
Heinrich-Buff-Ring 26–32; D-35392 Giessen, Germany
18
Tel. +49 641 99 37352 ; Fax. +49 641 99 37359
19
e-mail: [email protected]
20 21
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain JM-
22
1396T is KP657488.
1
1
Summary
2
A gram-negative, rod-shaped, non-spore-forming bacterium (strain JM-1396T) producing a
3
yellow pigment, was isolated from the healthy internal stem tissue of post-harvest cotton
4
(Gossypium hirsutum, cultivar ‘DES-119’) grown at the Plant Breeding Unit facility at the E.V.
5
Smith Research Center in Tallassee (Macon county), Alabama USA. 16S rRNA gene sequence
6
analysis of strain JM-1396T showed high sequence similarity values to the type strains of
7
Novosphingobium
8
Novosphingobium barchaimii (98.5%); sequence similarities to all other Novosphingobium
9
species type strains were below 98.3%. DNA-DNA pairing experiments of the DNA of strain
10
JM-1396T and N. mathurense SM117T, N. panipatense SM16T and N. barchaimii DSM 25411T
11
showed low similarity values of 8% (reciprocal: 7%), 24% (reciprocal 26%), and 19%
12
(reciprocal 25%), respectively.
13
Ubiquinone Q-10 was detected as the dominant quinone; the fatty acids C18:1 7c (71.0%) and
14
the typical 2-hydroxy fatty acid, C14:0 2-OH (11.7%), were detected as typical components. The
15
polar
16
phosphatedylethanolamine, sphingoglycolipid and phosphatidylcholine. The polyamine pattern
17
contained the major compound spermidine and only minor amounts of other polyamines.
18
All these data revealed that strain JM-1396T represents a new species of the genus
19
Novosphingobium. For this reason we propose the name Novosphingobium gossypii sp. nov.
20
with the type strain JM-1396T (= LMG 28605T = CCM 8569T = CIP 110884T).
lipid
mathurense,
profile
Novosphingobium
contained
the
panipatense
diagnostic
21
2
lipids
(both
98.6%),
and
diphosphatidylglycerol,
1
Representatives of the genus Novosphingobium were isolated from a large variety of
2
environmental sources including coastal and freshwater sediments and soil (Balkwill et al.,
3
1997; Sohn et al., 2004; Liu et al., 2005), surface water layers of lakes (Glaeser et al., 2009;
4
2013a, b), activated sludge/wastewater treatment plants (Neef et al., 1999; Fujii et al., 2003),
5
contaminated groundwater bioremediation reactor (Tiirola et al., 2002; 2005), and have also
6
been recently found associated with plants (Lin et al., 2014; Kämpfer et al., 2015). At the time
7
of writing 28 Novosphingobium species were described with validated names: N. acidiphilum
8
(Glaeser et al., 2009), N. aquaticum (Glaeser et al., 2013a), N. arabidopsis (Lin et al., 2014),
9
N. aromaticivorans (Balkwill et al., 1997), N. barchaimii (Niharika et al., 2013), N. capsulatum
10
(Yabuuchi et al., 1990), N. chloroacetimidivorans (Chen et al., 2014), N. fuchskuhlense
11
(Glaeser et al., 2013b), N. hassiacum (Kämpfer et al., 2002), N. indicum (Yuan et al., 2009),
12
N. kunmingense (Xie et al., 2014), N. lentum (Tiirola et al., 2005), N. lindaniclasticum (Saxena
13
et al., 2013), N. malaysiense (Lee et al., 2014a), N. mathurense and N. panipatense (Gupta et
14
al., 2009), N. naphthalenivorans (Suzuki & Hiraishi, 2007), N. nitrogenifigens (Addison et al.,
15
2007), N. pentaromativorans (Sohn et al., 2004), N. rosa (Takeuchi et al., 1995), N.
16
resinovorum (Lim et al., 2007), N. sediminicola (Baek et al., 2011), N. soli (Kämpfer et al.,
17
2011), N. stygium (Balkwill et al., 1997), N. subarcticum (which is a later subjective synonym
18
of N. resinivorum; Lim et al., 2007), N. subterraneum (Balkwill et al., 1997), N. taihuense (Liu
19
et al., 2005), and N. tardaugens (Fujii et al., 2003). Two further species proposals were recently
20
published, but the species names so far not validated, “N. ginsenosidimutans” (Kim et al., 2013)
21
and “N. aquiterrae” (Lee et al., 2014b).
22
Strain JM-1396T was isolated from the healthy internal stem tissue of post-harvest cotton
23
(Gossypium hirsutum, cultivar ‘DES-119’) grown at the Plant Breeding Unit facility at the E.V.
24
Smith Research Center in Tallassee (Macon county), Alabama USA. This isolate showed
25
microscopically single cells and formed small yellow colonies (70% are depicted. Nodes marked with circles were also conserved in the
7
maximum-parsimony tree, whereas larger circle were supported by a bootstrap value >70%.
8
Scale bar indicates 0.1 substitutions per 100 nucleotides.
9 10 11
Fig. 2.
12
Total polar lipid profile of strain JM-1396T after two-dimensional chromatography stained with
13
molybdatophosphoric acid. DPG, diphosphatidylglycerol; PE, phosphatidylethanolamine;
14
PDE, phosphatidyldimethylethanolamine; PG, phosphatidylglycerol, SGL, sphingoglycolipid,
15
PL1, PL2, unknown phospholipids, L1-L4, unknown lipids, AL1, unknown aminolipid, yPig,
16
yellow pigment.
17
19
Novosphingobium acidiphilum FSW06−204dT (EU336977) Novosphingobium nitrogenifigens Y88T (DQ448852) Novosphingobium taihuense T3−B9T (AY500142) T 98 Novosphingobium fuchskuhlense FNE08-7 (JN399172) T 87 Novosphingobium stygium IFO 16085 (AB025013) Novosphingobium sediminis YG−17T (FJ938155) Novosphingobium hassiacum W-51T (AJ416411) Novosphingobium lentum MT1T (AJ303009) Novosphingobium tardaugens ARI−1T (AB070237) Novosphingobium subterraneum IFO 16086T (AB025014) 98 Novosphingobium aquiterrae E−II−3T (FJ772064) Novosphingobium kunmingense 18−11HKT (JQ246446) Novosphingobium ginsenosidimutans FW−6T (JQ349046) Novosphingobium arabidopsis CC−ALB−2T (KC479803) Novosphingobium aromaticivorans DSM 12444T (CP000248) 99 Novosphingobium rhizosphaerae JM−1T (KM365125) Novosphingobium capsulatum GIFU11526T (D16147) Novosphingobium barchaimii LL02T (JN695619) Novosphingobium resinovorum NCIMB 8767T (EF029110) Novosphingobium lindaniclasticum LE124T (JN687581) Novosphingobium malaysiense MUSC 273T (KC907395) 94 Novosphingobium marinum LA53T (KJ708552) Novosphingobium indicum H25T (EF549586) 89 Novosphingobium mathurense SM117T (EF424403) Novosphingobium pentaromativorans US6−1T (AF502400) Novosphingobium gossypii JM−1396T (KP657488) Novosphingobium panipatense SM16T ( EF424402) Novosphingobium naphthalenivorans TUT562T (AB177883) Novosphingobium soli CC−TPE−1T (FJ425737) Novosphingobium chloroacetimidivorans BUT−14T (KF676669) Novosphingobium rosa IAM 14222T (D13945) Novosphingobium sediminicola HU1−AH51T (FJ177534) Novosphingobium aquaticum FNE08−86T (JN399173) 98 Sphingomicrobium astaxanthinifaciens CC−AMO−30BT (JX235675) 100 Sphingomicrobium lutaoense CC−TBT−3T (EU564841) 100 Sphingomicrobium marinum CC−AMZ−30MT (JX235672) Sphingomicrobium flavum CC−AMZ−30NT (JX393854)
Figure 1 100 Click here to download Figure: Fig-1.pdf
100
91
0.10
Figure 2 (NO BETTER RESOLUTION AVAILABLE) Click here to download Figure: Fig-2.docx
PL1
yPig L1 L2
DPG
PL2
PDE PG
SGL L3 AL1
L4
PE
