Oceanospirillales containing the DMSP lyase DddD are key utilisers of carbon from DMSP in coastal seawater

Liu, Jingli; Xue, Chun-Xu; Wang, Jinyan; Crombie, Andrew T.; Carrión, Ornella; Johnston, Andrew W. B.; Murrell, J. Colin; Liu, Ji; Zheng, Yanfen; Zhang, Xiao-Hua; Todd, Jonathan D.

doi:10.1186/s40168-022-01304-0

Microbiome

Table 1 Characteristics of DMSP-degrading bacterial strains isolated from seawater samples incubated with DMSP

From: Oceanospirillales containing the DMSP lyase DddD are key utilisers of carbon from DMSP in coastal seawater

Strain	Top-hit taxon identified by 16S rRNA gene sequences	Reference strain^a	Accession number of genomes from sequenced isolates	Homologues in reference strain or genome from sequenced isolate^b	DMS production rate^c	MeSH production^d	Growth on DMSP^e	Class
GY12	Litoreibacter albidus	DSM 26922		dddA, dddC, prpE, acuI, acuK, dmdA, dmdB, dmdC	ND	Y	N	Alphaproteobacteria
MB12-2	Neptunicoccus sediminis	CY02		dddP, prpE, acuI, acuK, dmdA, dmdB, dmdC	6 ± 2	ND	N	Alphaproteobacteria
GY7	Pseudophaeobacter arcticus	DSM 23566		dddW, dddA, dddC, prpE, acuI, acuN, acuK, dmdA, dmdB, dmdC, dmdD	558 ± 260	ND	N	Alphaproteobacteria
MB12-4	Sulfitobacter pontiacus	DSM 10014		dddL, dmdB, dmdC, dmdD	648 ± 153	ND	N	Alphaproteobacteria
GY16	Sulfitobacter pseudonitzschiae	H3		dddL, dddA, dddC, prpE, acuI, acuK, dmdB, dmdC, dmdD	201 ± 40	ND	N	Alphaproteobacteria
D12-10	Alteromonas stellipolaris	LMG 21861		dmdC	60 ± 6	ND	Y	Gammaproteobacteria
GY8	Marinobacter sediminum		JAGTWY000000000	dddL, dddA, dddC, prpE, dmdB, dmdC	4560 ± 785	ND	Y	Gammaproteobacteria
MC12-9	Marinobacter similis	A3d10		dddL, dddA, prpE, acuN, acuK, dmdC	86 ± 3	ND	Y	Gammaproteobacteria
GY20	Pseudoalteromonas hodoensis	H7			ND	Y	N	Gammaproteobacteria
D13-2	Cobetia amphilecti	KMM 296		dddD, dddA, dddC, dddT, prpE, acuI, acuK, dmdC, tmm	1342 ± 101	ND	N	Gammaproteobacteria
MC13-5	Cobetia litoralis		CP073342	dddD, dddA, dddC, dddT, prpE, acuI, dmdC, tmm	1316 ± 94	ND	Y	Gammaproteobacteria
GY6	Amphritea atlantica		CP073344, CP073345	dddD, prpE (2), acuI, acuK, dddB, dddC, dddT, dmdB (4), dmdC, tmm	1173 ± 208	ND	Y	Gammaproteobacteria
D13-1	Marinobacterium rhizophilum		CP073347	dddD, dddP, prpE (2), acuI, acuN, acuK, dddA, dddB, dddC, dddT, dmdB (2), dmdC	1039 ± 21	ND	Y	Gammaproteobacteria
MC13-7	Marinobacterium profundum	PAMC 27536		dddD, dddP, dddA, dddB, dddC, dddT, prpE (2), acuI, dmdB, dmdC	1132 ± 31	ND	Y	Gammaproteobacteria
GY1	Marinomonas atlantica	Cmf 18.22		dddD, dddB, dddC, prpE, acuI, dmdC	59 ± 30	ND	Y	Gammaproteobacteria
MB12-3	Marinomonas foliarum	CECT 7731		dddC, acuI, dmdC	11 ± 0.4	ND	N	Gammaproteobacteria
MB12-11	Marinomonas rhizomae		CP073343	dddD, dddB, dddC, dddT, acuI, dmdC	500 ± 36	ND	Y	Gammaproteobacteria
D13-4	Pseudomonas benzenivorans		CP073346	dddD, dddP, acuK, dddB, dddC, dddT, dmdB, dmdC	2462 ± 123	ND	Y	Gammaproteobacteria
GY22	Pseudomonas leptonychotis	CCM 8849		dddD, dddB, dddC, dddT, dmdB, dmdC	2350 ± 343	ND	Y	Gammaproteobacteria
GY17	Pseudomonas taeanensis	MS-3		dddD, dddP, dddB, dddC, dddT, acuI, dmdB, dmdC, tmm	829 ± 186	ND	Y	Gammaproteobacteria
GY15	Vibrio splendidus	10N.286.45		prpE, acuI, DMSOR	ND	Y	Y	Gammaproteobacteria

^aReference strain: most closely related strain with publicly available genome
^bNumber of prpE and dmdB genes in genomes with multiple copies are indicated in brackets
^cRate of DMSP-dependent DMS production expressed in nmol DMS mg protein⁻¹ h⁻¹
^dY, detectable MeSH production from DMSP. ND, not detected
^eY, growth on DMSP as sole carbon source (Student’s t-test, P < 0.05); N, no growth on DMSP as sole carbon source (P > 0.05)

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