微生物学报

Location	Station	Longitude	Latitude	Depth (m)	Sample collection section
F-cold seep	ROV272	119°17.142 9′	22°06.902 5′	1 127	Pushcore sediments (1−2 cm, 5−6 cm)
ROV272	119°17.142 9′	22°06.902 5′	1 127	Mussel (gill)
QY01	119°17.520 2′	22°06.499 6′	1 154	Gravity column sediments (0−5 cm, 5−10 cm, 50−55 cm)
CTD03	119°17.141 0′	22°06.932 0′	1 120	Surface water, 800 m water, bottom water
C2-	119°17.149 4′	22°06.894 0′	1 130	Gravity column sediments (0−5 cm, 120−125 cm, 235−240 cm)
C1	119°17.093 7′	22°06.965 8′	1 167	Gravity column sediments (0−3 cm, 54−57 cm, 105−108 cm)
ROV277	119°17.153 8′	22°06.925 4′	1 129	Shinkaia crosnieri (intestine, bristle and male gonad) Mussel (visceral mass, mantle and foot)
ROV277	119°17.140 6′	22°06.924 3′	1 124	Bottom water
ROV277	119°17.153 8′	22°06.904 2′	1 129	Pushcore sediments (0−2 cm, 6−8 cm, 8−10 cm)
ROV278	119°17.1615′	22°06.881 6′	1 135	Pushcore sediments (0−2 cm, 6−8 cm, 10−12 cm)
ROV278	119°17.157 9′	22°06.884 3′	1 135	Bottom water
ROV279	119°17.160 0′	22°06.920 5′	1 131	Pushcore sediments (0−2 cm, 6−8 cm)
ROV279	119°17.136 7′	22°06.927 6′	1 131	Polynoidae Tubeworm Shinkaia crosnieri (egg and gill)
ROV279	119°17.140 2′	22°06.925 2′	1 120	Water 5 m and 40 m from bottom
Yaeyama Knoll hydrothermal field	Hot1	124°22.382 0′	25°15.795 0′	2 157	1 000 m water, bottom water
RYSHW	124°22.366 9′	25°15.843 7′	2 157	Pushcore surface and bottom sediments
HZ04	124°22.363 2′	25°15.141 5′	2 279	Gravity column sediments (0−5 cm, 40−45 cm, 60−65 cm, 65−70 cm)

Location	Station	Longitude	Latitude	Depth (m)	Sample collection section
F-cold seep	ROV272	119°17.142 9′	22°06.902 5′	1 127	Pushcore sediments (1−2 cm, 5−6 cm)
ROV272	119°17.142 9′	22°06.902 5′	1 127	Mussel (gill)
QY01	119°17.520 2′	22°06.499 6′	1 154	Gravity column sediments (0−5 cm, 5−10 cm, 50−55 cm)
CTD03	119°17.141 0′	22°06.932 0′	1 120	Surface water, 800 m water, bottom water
C2-	119°17.149 4′	22°06.894 0′	1 130	Gravity column sediments (0−5 cm, 120−125 cm, 235−240 cm)
C1	119°17.093 7′	22°06.965 8′	1 167	Gravity column sediments (0−3 cm, 54−57 cm, 105−108 cm)
ROV277	119°17.153 8′	22°06.925 4′	1 129	Shinkaia crosnieri (intestine, bristle and male gonad) Mussel (visceral mass, mantle and foot)
ROV277	119°17.140 6′	22°06.924 3′	1 124	Bottom water
ROV277	119°17.153 8′	22°06.904 2′	1 129	Pushcore sediments (0−2 cm, 6−8 cm, 8−10 cm)
ROV278	119°17.1615′	22°06.881 6′	1 135	Pushcore sediments (0−2 cm, 6−8 cm, 10−12 cm)
ROV278	119°17.157 9′	22°06.884 3′	1 135	Bottom water
ROV279	119°17.160 0′	22°06.920 5′	1 131	Pushcore sediments (0−2 cm, 6−8 cm)
ROV279	119°17.136 7′	22°06.927 6′	1 131	Polynoidae Tubeworm Shinkaia crosnieri (egg and gill)
ROV279	119°17.140 2′	22°06.925 2′	1 120	Water 5 m and 40 m from bottom
Yaeyama Knoll hydrothermal field	Hot1	124°22.382 0′	25°15.795 0′	2 157	1 000 m water, bottom water
RYSHW	124°22.366 9′	25°15.843 7′	2 157	Pushcore surface and bottom sediments
HZ04	124°22.363 2′	25°15.141 5′	2 279	Gravity column sediments (0−5 cm, 40−45 cm, 60−65 cm, 65−70 cm)

Target genes	Primers name	Oligonucleotide (5′→3′)	Annealing temperature (℃)	References
dsyB	dsyB_F dsyB_R	CATGGGSTCSAAGGCSCTKTT GCAGRTARTCGCCGAAATCGTA	61	[29]
mmtN	mmtN_F mmtN_R	CCGAGGTGGTCATGAAYTTYGG GGATCACGCACACYTCRTGRTA	54	[34]
dddP	dddP_F dddP_R	AAYGAAATWGTTGCCTTTGA GCATDGCRTAAATCATATC	41	[42]
dddL	dddL_F dddL_R	CTGGGAATACGGCTACGAGA GTTCAAGATCAGCGATCCGG	53	[57]
dddD	dddD_F dddD_R	ACCAACGTCATTGCAGGACC TGTGCGTGTTCTTCCGGTG	56	[57]
dddX	dddX_F dddX_R	TTTGAAAACTCAGGCTTTTC TGAATATGGTAATGGTACTT	46	[48]
dmdA (A/1)	A/1_F A/1_R	ATGGTGATTTGCTTCAGTTTCT CCCTGCTTTGACCAACC	53	[58]
dmdA (A/2)	A/2_F A/2_R	CGATGAACATTGGTGGGTTTCTA GCCATTAGGTCGTCTGATTTTGG	59	[58]
dmdA (B/3)	B/3_F B/3_R	GATGTCTCCTGCCAACGTCAGGTCGA ACCGGGTCATTGATCATGCCTGCG	62	[58]
dmdA (C/2)	C/2_291F C/2_482R	AGATGAAAATGCTGGAATGATAAATG AAATCTTCAGACTTTGGACCTTG	50	[58]
dmdA (D/1)	D/1_268F D/1_356R	AGATGTTATTATTGTCCAATAATTGATG ATCCACCATCTATCTTCAGCTA	49	[58]
dmdA (E/2)	E/2_F E/2_R	CATGTTCAGATCTGGGACGT AGCGGCACATACATGCACT	57	[58]

Target genes	Primers name	Oligonucleotide (5′→3′)	Annealing temperature (℃)	References
dsyB	dsyB_F dsyB_R	CATGGGSTCSAAGGCSCTKTT GCAGRTARTCGCCGAAATCGTA	61	[29]
mmtN	mmtN_F mmtN_R	CCGAGGTGGTCATGAAYTTYGG GGATCACGCACACYTCRTGRTA	54	[34]
dddP	dddP_F dddP_R	AAYGAAATWGTTGCCTTTGA GCATDGCRTAAATCATATC	41	[42]
dddL	dddL_F dddL_R	CTGGGAATACGGCTACGAGA GTTCAAGATCAGCGATCCGG	53	[57]
dddD	dddD_F dddD_R	ACCAACGTCATTGCAGGACC TGTGCGTGTTCTTCCGGTG	56	[57]
dddX	dddX_F dddX_R	TTTGAAAACTCAGGCTTTTC TGAATATGGTAATGGTACTT	46	[48]
dmdA (A/1)	A/1_F A/1_R	ATGGTGATTTGCTTCAGTTTCT CCCTGCTTTGACCAACC	53	[58]
dmdA (A/2)	A/2_F A/2_R	CGATGAACATTGGTGGGTTTCTA GCCATTAGGTCGTCTGATTTTGG	59	[58]
dmdA (B/3)	B/3_F B/3_R	GATGTCTCCTGCCAACGTCAGGTCGA ACCGGGTCATTGATCATGCCTGCG	62	[58]
dmdA (C/2)	C/2_291F C/2_482R	AGATGAAAATGCTGGAATGATAAATG AAATCTTCAGACTTTGGACCTTG	50	[58]
dmdA (D/1)	D/1_268F D/1_356R	AGATGTTATTATTGTCCAATAATTGATG ATCCACCATCTATCTTCAGCTA	49	[58]
dmdA (E/2)	E/2_F E/2_R	CATGTTCAGATCTGGGACGT AGCGGCACATACATGCACT	57	[58]

Strain source	Strain number	Species	DMSP synthesis activity (nmol)	DMSP synthesis gene
ROV277 (bottom water)	LXJ078	Thalassospira profundimaris	0.75	mmtN^[34]
LXJ079	Thalassospira profundimaris	0.55	mmtN^[34]
QY01 (50−55 cm)	LXJ044	Sinomicrobium oceani	0.63
LXJ048	Idiomarina zobellii	0.57
Mussel (gill)	LXJ091	Alteromonas tagae	0.42
LXJ093	Alteromonas tagae	0.30
ROV279 (water 5 m from bottom)	LXJ106	Vibrio chagasii	0.73
LXJ108	Pseudooceanicola marinus	8.23	dsyB^[29]

Strain source	Strain number	Species	DMSP synthesis activity (nmol)	DMSP synthesis gene
ROV277 (bottom water)	LXJ078	Thalassospira profundimaris	0.75	mmtN^[34]
LXJ079	Thalassospira profundimaris	0.55	mmtN^[34]
QY01 (50−55 cm)	LXJ044	Sinomicrobium oceani	0.63
LXJ048	Idiomarina zobellii	0.57
Mussel (gill)	LXJ091	Alteromonas tagae	0.42
LXJ093	Alteromonas tagae	0.30
ROV279 (water 5 m from bottom)	LXJ106	Vibrio chagasii	0.73
LXJ108	Pseudooceanicola marinus	8.23	dsyB^[29]

Strain source	Strain number	Species	DMSP synthesis activity (nmol)	DMSP synthesis gene
Hot1 (bottom water)	LXJ035	Alteromonas macleodii	0.29
ROV279 (water 40 m from bottom)	LXJ021	Thalassospira profundimaris	1.84	mmtN^[34]
ROV277 (bottom water)	LXJ027	Thalassospira profundimaris	2.86	mmtN^[34]
ROV272 (5−6 cm)	LXJ008	Thalassospira profundimaris	0.30	mmtN^[34]
ROV277 (8−10 cm)	LXJ110	Idiomarina loihiensis	0.47
Shinkaia crosnieri (bristle)	LXJ113	Pseudoalteromonas shioyasakiensis	0.41
LXJ117	Pseudooceanicola marinus	3.18	dsyB^[29]

Strain source	Strain number	Species	DMSP synthesis activity (nmol)	DMSP synthesis gene
Hot1 (bottom water)	LXJ035	Alteromonas macleodii	0.29
ROV279 (water 40 m from bottom)	LXJ021	Thalassospira profundimaris	1.84	mmtN^[34]
ROV277 (bottom water)	LXJ027	Thalassospira profundimaris	2.86	mmtN^[34]
ROV272 (5−6 cm)	LXJ008	Thalassospira profundimaris	0.30	mmtN^[34]
ROV277 (8−10 cm)	LXJ110	Idiomarina loihiensis	0.47
Shinkaia crosnieri (bristle)	LXJ113	Pseudoalteromonas shioyasakiensis	0.41
LXJ117	Pseudooceanicola marinus	3.18	dsyB^[29]

Strain source	Strain number	Species	DMSP demethylation activity	DMSP cleavage activity (nmol/h)
DMSP cleavage rate over 0.10 nmol/h. DMSP lysed strains that can produce MeSH are indicated by “+”, and those cannot produce MeSH are indicated by “−”.
CTD03 (bottom water)	LXJ198	Hyphomonas oceanitis	−	1.58
LXJ143	Pseudohoeflea suaedae	−	1.57
LXJ144	Pseudomonas stutzeri	−	1.27
LXJ145	Pseudohoeflea suaedae	−	1.62
LXJ197	Staphylococcus cohnii	−	0.12
LXJ199	Nesterenkonia halobia	−	0.17
C1 (105−108 cm)	LXJ231	Sulfitobacter pontiacus	−	1.83
LXJ232	Sulfitobacter pontiacus	−	1.83
ROV278 (bottom water)	LXJ189	Glutamicibacter creatinolyticus	−	1.35
LXJ190	Bacillus spizizenii	−	1.21
LXJ268	Alcanivorax dieselolei	−	1.89
LXJ269	Marinobacter nauticus	−	0.20
Shinkaia crosnieri (male gonad)	LXJ165	Marinobacter flavimaris	+	1.82
LXJ166	Marinobacter flavimaris	+	1.74
LXJ177	Glutamicibacter creatinolyticus	−	0.15
Mussel (visceral mass)	LXJ194	Hyphomonas oceanitis	−	1.67
LXJ155	Glutamicibacter creatinolyticus	−	0.22
LXJ193	Glutamicibacter creatinolyticus	−	0.13
ROV278 (6−8 cm)	LXJ258	Glutamicibacter creatinolyticus	−	0.39
LXJ260	Brachybacterium paraconglomeratum	−	0.92
LXJ195	Glutamicibacter creatinolyticus	−	0.18
ROV279 (6−8 cm)	LXJ261	Staphylococcus equorum subsp. linens	−	0.91
LXJ262	Staphylococcus cohnii	−	0.52
RYSHW (bottom sediments)	LXJ271	Shewanella xiamenensis	+	0.90
LXJ270	Georgenia muralis	−	0.12
LXJ273	Shewanella seohaensis	−	0.20
CTD03 (surface water)	LXJ186	Micrococcus endophyticus	−	0.12
CTD03 (800 m water)	LXJ200	Pseudohoeflea suaedae	−	0.15
LXJ245	Exiguobacterium mexicanum	−	0.11
Hot1 (5 m water)	LXJ205	Pseudohoeflea suaedae	−	0.16
Hot1 (1 000 m water)	LXJ148	Pseudohoeflea suaedae	−	0.30
LXJ149	Idiomarina loihiensis	−	0.14
QY01 (5−10 cm)	LXJ134	Glutamicibacter creatinolyticus	−	0.14
LXJ214	Micrococcus endophyticus	−	0.15
LXJ215	Micrococcus luteus	−	0.15
C2- (0−5 cm)	LXJ136	Glutamicibacter creatinolyticus	−	0.19
C2- (235−240 cm)	LXJ182	Glutamicibacter creatinolyticus	−	0.13
C1 (0−3 cm)	LXJ201	Paracoccus halotolerans	−	0.22
LXJ202	Glutamicibacter creatinolyticus	−	0.17
LXJ223	Kocuria palustris	−	0.18
LXJ224	Halomonas meridiana	−	0.19
C1 (54−57 cm)	LXJ137	Glutamicibacter creatinolyticus	−	0.18
ROV277 (0−2 cm)	LXJ241	Staphylococcus equorum subsp. linens	−	0.19
ROV278 (0−2 cm)	LXJ251	Marinobacter nauticus	−	0.13
LXJ253	Micrococcus luteus	−	0.28
ROV279 (water 5 m from bottom)	LXJ181	Micrococcus luteus	−	0.15
Shinkaia crosnieri (bristle)	LXJ170	Micrococcus endophyticus	−	0.12
Shinkaia crosnieri (egg)	LXJ159	Glutamicibacter creatinolyticus	−	0.21
LXJ162	Staphylococcus equorum subsp. linens	−	0.13
LXJ163	Kocuria rosea	−	0.12
LXJ176	Glutamicibacter arilaitensis	−	0.14
Mussel (gill)	LXJ152	Glutamicibacter creatinolyticus	−	0.12
Mussel (mantle)	LXJ158	Glutamicibacter creatinolyticus	−	0.24
Mussel (foot)	LXJ156	Glutamicibacter creatinolyticus	−	0.19
LXJ157	Glutamicibacter creatinolyticus	−	0.22

Strain source	Strain number	Species	DMSP demethylation activity	DMSP cleavage activity (nmol/h)
DMSP cleavage rate over 0.10 nmol/h. DMSP lysed strains that can produce MeSH are indicated by “+”, and those cannot produce MeSH are indicated by “−”.
CTD03 (bottom water)	LXJ198	Hyphomonas oceanitis	−	1.58
LXJ143	Pseudohoeflea suaedae	−	1.57
LXJ144	Pseudomonas stutzeri	−	1.27
LXJ145	Pseudohoeflea suaedae	−	1.62
LXJ197	Staphylococcus cohnii	−	0.12
LXJ199	Nesterenkonia halobia	−	0.17
C1 (105−108 cm)	LXJ231	Sulfitobacter pontiacus	−	1.83
LXJ232	Sulfitobacter pontiacus	−	1.83
ROV278 (bottom water)	LXJ189	Glutamicibacter creatinolyticus	−	1.35
LXJ190	Bacillus spizizenii	−	1.21
LXJ268	Alcanivorax dieselolei	−	1.89
LXJ269	Marinobacter nauticus	−	0.20
Shinkaia crosnieri (male gonad)	LXJ165	Marinobacter flavimaris	+	1.82
LXJ166	Marinobacter flavimaris	+	1.74
LXJ177	Glutamicibacter creatinolyticus	−	0.15
Mussel (visceral mass)	LXJ194	Hyphomonas oceanitis	−	1.67
LXJ155	Glutamicibacter creatinolyticus	−	0.22
LXJ193	Glutamicibacter creatinolyticus	−	0.13
ROV278 (6−8 cm)	LXJ258	Glutamicibacter creatinolyticus	−	0.39
LXJ260	Brachybacterium paraconglomeratum	−	0.92
LXJ195	Glutamicibacter creatinolyticus	−	0.18
ROV279 (6−8 cm)	LXJ261	Staphylococcus equorum subsp. linens	−	0.91
LXJ262	Staphylococcus cohnii	−	0.52
RYSHW (bottom sediments)	LXJ271	Shewanella xiamenensis	+	0.90
LXJ270	Georgenia muralis	−	0.12
LXJ273	Shewanella seohaensis	−	0.20
CTD03 (surface water)	LXJ186	Micrococcus endophyticus	−	0.12
CTD03 (800 m water)	LXJ200	Pseudohoeflea suaedae	−	0.15
LXJ245	Exiguobacterium mexicanum	−	0.11
Hot1 (5 m water)	LXJ205	Pseudohoeflea suaedae	−	0.16
Hot1 (1 000 m water)	LXJ148	Pseudohoeflea suaedae	−	0.30
LXJ149	Idiomarina loihiensis	−	0.14
QY01 (5−10 cm)	LXJ134	Glutamicibacter creatinolyticus	−	0.14
LXJ214	Micrococcus endophyticus	−	0.15
LXJ215	Micrococcus luteus	−	0.15
C2- (0−5 cm)	LXJ136	Glutamicibacter creatinolyticus	−	0.19
C2- (235−240 cm)	LXJ182	Glutamicibacter creatinolyticus	−	0.13
C1 (0−3 cm)	LXJ201	Paracoccus halotolerans	−	0.22
LXJ202	Glutamicibacter creatinolyticus	−	0.17
LXJ223	Kocuria palustris	−	0.18
LXJ224	Halomonas meridiana	−	0.19
C1 (54−57 cm)	LXJ137	Glutamicibacter creatinolyticus	−	0.18
ROV277 (0−2 cm)	LXJ241	Staphylococcus equorum subsp. linens	−	0.19
ROV278 (0−2 cm)	LXJ251	Marinobacter nauticus	−	0.13
LXJ253	Micrococcus luteus	−	0.28
ROV279 (water 5 m from bottom)	LXJ181	Micrococcus luteus	−	0.15
Shinkaia crosnieri (bristle)	LXJ170	Micrococcus endophyticus	−	0.12
Shinkaia crosnieri (egg)	LXJ159	Glutamicibacter creatinolyticus	−	0.21
LXJ162	Staphylococcus equorum subsp. linens	−	0.13
LXJ163	Kocuria rosea	−	0.12
LXJ176	Glutamicibacter arilaitensis	−	0.14
Mussel (gill)	LXJ152	Glutamicibacter creatinolyticus	−	0.12
Mussel (mantle)	LXJ158	Glutamicibacter creatinolyticus	−	0.24
Mussel (foot)	LXJ156	Glutamicibacter creatinolyticus	−	0.19
LXJ157	Glutamicibacter creatinolyticus	−	0.22

南海F-冷泉和冲绳海槽热液区可培养二甲基巯基丙酸内盐合成与降解细菌的分离鉴定及其多样性

PDF下载

高熠 ¹^,^# , 刘秀杰 ¹^,^# , 刘仪 ¹ , 李倩宇 ¹ , 郭瑞红 ¹ , 张晓华 ¹^,²^,³^,⁴ , 张蕴慧 ¹^,²^,³^,⁴^,^*

微生物学报 | 水圈微生物专栏 2024,64(12): 4515-4536

收起

微生物学报 | 水圈微生物专栏 2024, 64(12): 4515-4536

南海F-冷泉和冲绳海槽热液区可培养二甲基巯基丙酸内盐合成与降解细菌的分离鉴定及其多样性

全屏

高熠¹^,^#, 刘秀杰¹^,^#, 刘仪¹, 李倩宇¹, 郭瑞红¹, 张晓华¹^,²^,³^,⁴, 张蕴慧¹^,²^,³^,⁴^,^*

作者信息

1 中国海洋大学海洋生命学院, 山东青岛 266003

2 青岛海洋科学技术中心, 海洋生态与环境科学功能实验室, 山东青岛 266237

3 中国海洋大学, 深海圈层与地球系统前沿科学中心, 山东青岛 266100

4 中国海洋大学, 海洋生物多样性与进化研究所, 山东青岛 266003

Isolation, identification, and diversity analysis of culturable DMSP-synthesizing and -degrading bacteria in F-cold seep of the South China Sea and hydrothermal fields of the Okinawa Trough

Yi GAO¹^,^#, Xiujie LIU¹^,^#, Yi LIU¹, Qianyu LI¹, Ruihong GUO¹, Xiaohua ZHANG¹^,²^,³^,⁴, Yunhui ZHANG¹^,²^,³^,⁴^,^*

Affiliations

1 College of Marine Life Sciences, Ocean University of China, Qingdao 266003, Shandong, China

2 Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, Shandong, China

3 Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, Shandong, China

4 Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, Shandong, China

出版时间: 2024-12-04 doi: 10.13343/j.cnki.wsxb.20240708

文章导航

摘要

收起

【目的】冷泉和热液是海洋中典型的化能生态系统，其独特的理化特征孕育了特殊的微生物类群。二甲基巯基丙酸内盐(dimethylsulfoniopropionate, DMSP)是地球上最丰富的有机硫化合物之一，多种海洋细菌能够合成与降解DMSP，在驱动海洋碳、硫元素循环过程中发挥重要作用。本研究对南海F-冷泉和冲绳海槽热液区的DMSP合成与降解细菌进行了分离鉴定，分析其多样性与分布，拓展了对海洋中DMSP代谢细菌的认识。【方法】选取南海F-冷泉和冲绳海槽Yaeyama Knoll热液区不同深度水体、沉积物和动物为研究对象，利用3种富集培养基(甲硫氨酸添加、高盐低氮条件用于富集DMSP合成细菌，DMSP添加用于富集DMSP降解细菌)和2216E分离培养基进行细菌的富集与分离培养。通过16S rRNA基因测序确定菌株分类地位，并检测代表菌株的DMSP合成与降解能力。【结果】本研究共获得874株可培养细菌，其中γ-变形菌纲(Gammaproteobacteria)为3种培养基中获得的优势纲；海杆菌属(Marinobacter)为优势属。经富集后冷泉样品的可培养菌株数量和多样性均高于热液样品。冷泉来源的14株DMSP合成细菌分属于7个属，其中5株属于近海螺旋菌属(Thalassospira)且含有DMSP合成基因mmtN，2株属于假栖大洋菌属(Pseudooceanicola)并含有dsyB。冷泉来源的130株DMSP降解细菌分属于39个属，谷氨酸杆菌属(Glutamicibacter)为最优势属(24株)且不含已知DMSP降解基因。热液区来源的DMSP合成细菌仅1株，降解细菌18株，均远少于冷泉样品。具有DMSP裂解途径的菌株占降解细菌总数(148株)的98.6%，其中55株裂解活性较强且以放线菌纲(Actinobacteria)为主。在40株不同种且DMSP降解能力较强的菌株中，9株含有已知的裂解基因，3株含有已知的脱甲基基因。【结论】南海F-冷泉和冲绳海槽热液区存在丰富的DMSP合成与降解细菌，包括多种含有潜在新型DMSP合成/降解基因的细菌类群。本研究为进一步深入理解化能生态系统中微生物驱动的有机硫循环提供了基础。

关键词

二甲基巯基丙酸内盐 / 合成与降解 / 冷泉 / 热液区 / 细菌多样性

Abstract

收起

[Objective] Cold seeps and hydrothermal fields are typical chemosynthetic ecosystems in the ocean. With distinctive physicochemical properties, they harbor unique microbial communities. Dimethylsulfoniopropionate (DMSP), one of the most abundant organic sulfur-containing compounds on Earth, is synthesized and degraded by a variety of marine bacteria, which plays an important role in driving carbon and sulfur cycles in the ocean. In this study, we isolated and identified DMSP-synthesizing and degrading bacteria from the F-cold seep of the South China Sea and hydrothermal fields of the Okinawa Trough and analyzed their diversity and distribution, aiming to expand the understanding of these bacteria in the ocean. [Methods] Water, sediment, and animal samples were collected at different depths from both the F-cold seep of the South China Sea and the Yaeyama Knoll hydrothermal field of the Okinawa Trough. Three enrichment media (l-methionine addition and high salinity and low nitrogen for DMSP-synthesizing bacteria; DMSP addition for DMSP-degrading bacteria) and the 2216E medium were used for the enrichment and isolation of bacteria. The taxonomic status of strains was determined by 16S rRNA gene sequencing, and the abilities of representative strains to synthesize or degrade DMSP were assessed. [Results] A total of 874 culturable strains were obtained. Gammaproteobacteria emerged as the dominant class in the three media, and Marinobacter was the most abundant genus. The number and diversity of culturable strains obtained from cold seep samples after enrichment were higher than those from the hydrothermal field. The 14 strains of DMSP-synthesizing bacteria from the cold seep belonged to 7 genera, including 5 Thalassospira strains carrying the DMSP synthesis gene mmtN and 2 Pseudooceanicola strains carrying dsyB. A total of 130 DMSP-degrading bacterial strains were obtained from the cold seep, belonging to 39 genera, among which Glutamicibacter was the most abundant genus (24 strains) without known genes associated with DMSP degradation. There was only 1 strain of DMSP-synthetizing bacteria and 18 strains of DMSP-degrading bacteria from the hydrothermal field, both were much fewer than those from the cold seep. The strains with DMSP cleavage pathway accounted for 98.6% of the total DMSP-degrading strains (148), among which 55 strains had strong cleavage activity and were mainly Actinobacteria. Among the 40 strains with strong DMSP-degrading activity, 9 strains contained known cleavage genes and 3 strains contained known demethylation genes. [Conclusion] Abundant DMSP-synthesizing and -degrading bacteria exist in F-cold seep of the South China Sea and hydrothermal fields of the Okinawa Trough, including a variety of bacterial groups carrying potential novel DMSP synthesis/degradation genes. This study provides a basis for further understanding the microbial-driven organosulfur cycling in chemosynthetic ecosystems.

Key words

dimethylsulfoniopropionate / synthesis and degradation / cold seep / hydrothermal field / bacterial diversity

引用本文

高熠, 刘秀杰, 刘仪, 李倩宇, 郭瑞红, 张晓华, 张蕴慧. 南海F-冷泉和冲绳海槽热液区可培养二甲基巯基丙酸内盐合成与降解细菌的分离鉴定及其多样性. 微生物学报, 2024 , 64 (12) : 4515 -4536 . DOI: 10.13343/j.cnki.wsxb.20240708

Yi GAO, Xiujie LIU, Yi LIU, Qianyu LI, Ruihong GUO, Xiaohua ZHANG, Yunhui ZHANG. Isolation, identification, and diversity analysis of culturable DMSP-synthesizing and -degrading bacteria in F-cold seep of the South China Sea and hydrothermal fields of the Okinawa Trough[J]. Acta Microbiologica Sinica, 2024 , 64 (12) : 4515 -4536 . DOI: 10.13343/j.cnki.wsxb.20240708

正文

收起

冷泉(cold seep)是富含CH₄的流体从海底深部向海底表面渗漏或喷发所形成的特殊地质构造^[1]。目前全球已知的冷泉达数百个，主要分布于大陆边缘，比如墨西哥湾、黑海和东地中海等^[2]。F-冷泉位于中国南海北部大陆边缘，水深约1 125 m^[3-5]，是中国海域发现的3个活动冷泉之一^[6]。热液喷口(hydrothermal vent)指通过海底裂隙向下渗流的海水与被岩浆加热的岩石相互作用，进而以热液流体的形式喷发出海底而形成的独特环境^[7]。目前全球已发现500多处活动热液喷口^[8]，其中，Yaeyama Knoll热液区为中国东海冲绳海槽(Okinawa Trough)的15个热液区之一，其喷口水深约2 190 m，温度可达364 ℃，是冲绳海槽中最深且温度最高的喷口^[9]。冷泉和热液区都是深海中典型的化能合成生态系统，且2种环境中富含H₂S等还原性气体，在硫元素循环中起着重要作用，参与硫循环的功能基因在这些区域广泛分布^[10]。

二甲基巯基丙酸内盐(dimethylsulfoniopropionate, DMSP)是地球上含量最丰富的有机含硫化合物之一^[11]，首次在多管藻(Polysiphonia)中被发现^[12]。DMSP年产量高达10⁹ t (约7×10¹³ mol)^[13]，占全球初级生产力的1%−10%^[14]。DMSP可作为生物体的渗透压保护剂^[15]、高压保护剂^[16]、抗氧化剂^[17]、冷冻保护剂^[18]、化学引诱剂^[19]、信号分子^[20]、细菌毒力因子合成前体^[21]，并且是海洋生态系统中的重要碳源和硫源^[22]。除此之外，DMSP的裂解产物二甲基硫(dimethylsulfide, DMS)进入大气后能对全球变暖产生负调控作用^[22]。目前，已发现浮游植物^[23]、大型藻类^[24]、珊瑚^[25]、盐生被子植物^[26-28]和异养细菌^[29]能够合成DMSP，并阐明了3条DMSP的生物合成途径：甲基化途径^[28]、转氨基途径^[30]以及脱羧基途径^[31]。一系列参与DMSP合成的关键基因陆续被鉴定，包括dsyB^[29]、DSYB^[32]、TpMMT^[33]、mmtN^[34]、burB^[21]、dsyGD/dsyG^[35]和DSYE^[35]。此外，海洋异养细菌还是DMSP的最主要降解者^[36-37]。DMSP降解途径包括脱甲基途径^[38]、裂解途径^[39]和氧化途径^[40]，目前已发现一系列DMSP降解基因，比如裂解基因dddL^[41]、dddP^[42]、dddQ^[43]、dddW^[44]、dddY^[45]、dddK^[46]、dddD^[47]、dddX^[48]、dddU^[49]和脱甲基基因dmdA^[14]。已有的一系列研究探究了中国东海^[50-51]、中国南海^[52]、马里亚纳海沟^[16]、北极和南极^[53]等环境中DMSP合成与降解细菌的多样性，但尚未见深海化能生态系统冷泉和热液区DMSP合成与降解细菌多样性的研究，这2种环境中均存在活跃的硫代谢过程，以及与硫代谢相关的特殊微生物类群，因此很可能存在新型DMSP合成与降解细菌、途径及基因有待进一步发掘。

本研究拟通过细菌分离培养等方法，探索南海F-冷泉和冲绳海槽Yaeyama Knoll热液区DMSP合成与降解细菌的多样性，丰富对深海化能生态系统DMSP合成与降解细菌多样性的认识，同时为筛选新的DMSP合成与降解途径及基因提供菌株资源。

1 材料与方法

收起

1.1 样品采集

本研究所用样品于2022年5月搭载中国海洋大学“东方红3号”综合科学考察船采集自南海F-冷泉和冲绳海槽Yaeyama Knoll热液区。获得的多个层次的海水、沉积物及动物样品，站位及样品信息如表1所示。其中站位Hot1、RYSHW和HZ04位于冲绳海槽Yaeyama Knoll热液区，其余站位均位于南海F-冷泉。

1.2 富集培养和培养基

获得海水、沉积物及动物样品(现场解剖获得各个动物组织)后，立即在现场进行富集培养。分别将1 mL海水样品、0.1 g沉积物样品或动物组织用50 mL无菌生理盐水(质量分数为0.85%)稀释，吸取1 mL稀释液分别加入3种50 mL液体培养基[marine basal medium (MBM)+l-methionine (l-Met)混合培养基、高盐低氮MBM+l-Met混合培养基、MBM+DMSP混合培养基]中，在16 ℃以110 r/min振荡培养。其中MBM+l-Met混合培养基和高盐低氮MBM+l-Met混合培养基用于富集DMSP合成细菌，MBM+DMSP混合培养基用于富集DMSP降解细菌。

MBM培养基(PSU 35)：250 mL MBM Basal溶液，35 g海盐，50 mL 50 mg/mL FeEDTA贮存液，10 mL 1 mol/L NH₄Cl贮存液，与680 mL ddH₂O混合均匀，再分装成每份50 mL，121 ℃灭菌20 min。高盐低氮MBM培养基(PSU 50)：250 mL MBM Basal溶液，50 g海盐，50 mL 50 mg/mL FeEDTA贮存液，1 mL 1 mol/L NH₄Cl贮存液，与680 mL ddH₂O混合均匀，再分装成每份50 mL，121 ℃灭菌20 min。每50 mL培养基随后在无菌超净台加入50 μL 20×混合维生素贮存液，500 μL混合碳源贮存液，250 μL 100 mmol/L l-Met (终浓度0.5 mmol/L)或500 μL 100 mmol/L DMSP (终浓度1 mmol/L)。MBM Basal溶液：34.61 g Tris，0.17 g K₂HPO₄，加入适量ddH₂O使其完全溶解，利用浓HCl调节pH值为7.5后加ddH₂O定容为1 L，121 ℃灭菌20 min，室温保存。1 000×混合维生素贮存液：20 mg生物素(biotin, VH)，20 mg叶酸(folic acid)，100 mg盐酸吡哆醇(pyridoxine-HCl, VB₆-HCl)，50 mg二水合盐酸硫胺素(thiamine-HCl·2H₂O, VB₁-HCl·2H₂O)，50 mg核黄素(riboflavin, VB₂)，50 mg烟酸(nicotinic acid)，50 mg d-泛酸钙(d-Ca-pantothenate)，1 mg氰钴胺素(cyanocobalamine, VB₁₂)，50 mg对氨基苯甲酸(p-aminobenzoic acid)，50 mg硫辛酸(lipoic-acid)，溶于1 L无菌ddH₂O，用0.22 μm滤膜过滤除菌并50 mL分装，贮存于−20 ℃。混合碳源贮存液：54 g六水合琥珀酸钠，36.3 g葡萄糖，68.4 g蔗糖，22 g丙酮酸钠，14.6 mL丙三醇，溶解于985.4 mL ddH₂O中，调节pH值至7.5后，用0.22 μm滤膜过滤除菌并50 mL分装，贮存于4 ℃。

1.3 DMSP合成情况检测

用MBM+l-Met混合培养基和高盐低氮MBM+l-Met混合培养基富集培养DMSP合成细菌，以16 ℃、110 r/min培养14 d后，在无菌超净台中吸取200 μL菌液至2 mL棕色色谱瓶中，瓶身平放后将100 μL 10 mol/L NaOH加至瓶颈，旋紧瓶盖后正立色谱瓶，使碱液与菌液混合。将色谱瓶置于28 ℃恒温摇床以170 r/min振荡2 h，使菌液中的DMSP充分裂解为DMS气体。利用气相色谱仪(安捷伦科技有限公司)采用顶空测定法抽取顶空DMS气体，从而检测DMSP合成细菌富集培养情况(DMSP经裂解生成相同物质的量的DMS气体)。

1.4 菌株的分离纯化及鉴定

1.4.1 菌株的分离纯化

将富集培养后的DMSP降解细菌菌液与经气相色谱仪检测后DMSP合成量较高的合成细菌菌液在无菌超净台中用生理盐水等梯度稀释为6个浓度梯度(10⁻¹−10⁻⁶)，吸取10⁻⁴、10⁻⁵、10⁻⁶这3个浓度梯度的菌液各150 μL，涂布到2216E培养基^[54]上，在28 ℃恒温培养箱中培养24−48 h，随后挑取不同形态的单菌落进行三区划线，继续放置在28 ℃恒温培养箱中培养24−48 h，待第一次纯化的单菌落生长出来后再进行2次分离纯化和培养以获得纯菌落。

1.4.2 菌株的物种鉴定

采用煮沸法并辅以酚-氯仿法^[55]提取纯化菌株的DNA。利用通用引物B8F (5′-AGAGTTT GATCCTGGCTCAG-3′)和B1510R (5′-GGTTAC CTTGTTACGACTT-3′)^[56]对细菌的16S rRNA基因进行PCR扩增。PCR扩增体系(30 μL)：2×Taq Plus Master Mix II (Dye Plus) 15 μL，ddH₂O 13.2 μL，通用引物B8F和B1510R各0.3 μL，模板DNA 1.2 μL。PCR扩增程序：95 ℃预变性5 min；95 ℃变性1 min，55 ℃退火1 min，72 ℃延伸1.5 min，共30个循环；72 ℃再延伸10 min。随后将PCR扩增产物送至生工生物工程(上海)股份有限公司进行测序。在Chromas软件上对获得的原始16S rRNA基因序列进行剪切，选取650 bp的高质量核酸序列上传至EzBioCloud网站(http://www.ezbiocloud.net/)进行序列比对，得到最相似菌株的详细信息、相似度和完整度等以此鉴定测序菌株的分类地位。

1.5 菌株DMSP合成与降解能力检测

1.5.1 菌株DMSP合成能力检测

选择同一样品来源和富集条件下不同种的代表性可培养菌株进行DMSP合成能力的检测。在2 mL棕色色谱瓶中加入300 μL MBM+ l-Met混合培养基，挑取适量纯菌落置于色谱瓶中，与培养基充分混合后旋紧瓶盖；同时在1.5 mL无菌EP管中加入500 μL MBM+l-Met混合培养基，挑取适量纯菌落置于EP管中，与培养基充分混合后盖紧管盖；以具有强DMSP合成能力的菌株Labrenzia aggregate LZB033作为阳性对照；以不加菌的培养基作为空白对照，每组均设置3个平行。将加完菌的色谱瓶和EP管置于28 ℃恒温摇床中以170 r/min避光培养24 h，直接利用气相色谱仪测定色谱瓶中产生的甲硫醇(methanethiol, MeSH)和/或DMS，以确定菌株是否利用l-Met为底物直接产生MeSH和/或DMS；同时在避光条件下吸取200 μL EP管中培养24 h的菌液到色谱瓶中，平放瓶身后将100 μL 10 mol/L NaOH加至瓶颈，将瓶盖拧紧后正置瓶身，置于28 ℃恒温摇床中以170 r/min再振荡2 h，使菌液中的DMSP充分裂解为DMS，用气相色谱仪测定色谱瓶中产生的DMS及其峰面积，以确定纯化菌株是否利用l-Met为底物产生DMSP。最终判断菌株是否具有DMSP合成能力。

1.5.2 菌株DMSP降解能力检测

选择同一样品来源和富集条件下不同种的代表性可培养菌株进行DMSP降解能力的检测。在2 mL色谱瓶中加入300 μL MBM+DMSP混合培养基，挑取适量纯菌落置于色谱瓶中，与培养基充分混合后旋紧瓶盖；同时在2 mL色谱瓶中加入300 μL不加DMSP的MBM培养基，挑取适量纯菌落置于色谱瓶中，充分混合后旋紧瓶盖；以不加菌液的MBM+DMSP混合培养基为空白对照，每组均设置3个平行，28 ℃、170 r/min培养24 h，利用气相色谱仪测定色谱瓶中产生的MeSH和/或DMS气体，以此确定菌株是否将DMSP降解为MeSH和/或DMS。

1.5.3 DMSP浓度标准曲线绘制

DMSP浓度标准曲线采用梯度浓度的DMSP标准溶液经碱解生成DMS的方法绘制。配制DMSP终浓度为750 mmol/L的DMSP一级标准溶液，按梯度稀释为终浓度75 000、7 500、750、75、7.5 μmol/L的DMSP系列标准溶液。取7.5 mmol/L 2 μL，750 μmol/L 2、4、8 μL，75 μmol/L 4、8 μL，7.5 μmol/L 4、8 μL，分别加至2 mL棕色色谱瓶底部，将相应体积(体系体积之和为300 μL)的10 mol/L NaOH加到色谱瓶颈部，小心将瓶盖拧紧后正置瓶身，28 ℃、170 r/min振荡2 h，使标准溶液中的DMSP充分裂解为DMS气体，用气相色谱仪测定色谱瓶中产生的顶空DMS气体峰面积，进而计算DMS/P物质的量和净峰面积关系的标准曲线，如公式(1)所示，其中R²=0.999。

(1)

1.6 菌株DMSP合成与降解基因鉴定

利用已知DMSP合成与降解基因的简并引物(表2)，对具有DMSP合成与降解能力的菌株进行简并PCR。PCR扩增体系(30 μL)：2×Taq Plus Master Mix II (Dye Plus) 15 μL，ddH₂O 13.2 μL，正、反引物各0.3 μL，模板DNA 1.2 μL。PCR扩增程序：95 ℃预变性5 min；95 ℃变性30 s，T_m−5 ℃退火30 s，72 ℃延伸20 s，共35个循环；72 ℃延伸10 min。PCR扩增产物进行琼脂糖凝胶电泳并切胶回收后送至生工生物工程(上海)股份有限公司进行目的基因测序，在NCBI数据库中查找各个已知DMSP合成与降解基因的序列，与测序所得序列进行BLAST分析，以确定具有DMSP合成与降解能力的菌株中是否含有已知的DMSP合成与降解基因。

2 结果与分析

收起

2.1 富集培养后菌群的DMSP产量

总计20瓶DMSP合成细菌富集样品(MBM+l-Met混合培养基7瓶，高盐低氮MBM+l-Met混合培养基13瓶)中的DMSP浓度明显升高(> 1.5 μmol/L)，其中19瓶为冷泉样品，热液区样品仅有Hot1 (底层水) 1瓶。MBM+l-Met混合培养基的7瓶富集培养样品来源于冷泉水体、沉积物和贻贝。其中ROV277 (底层水)富集后菌群产生的DMSP浓度最高，为14.35 μmol/L。贻贝内脏团和沉积物QY01 (50−55 cm)最低，为1.9 μmol/L。沉积物C2- (0−5 cm)富集后菌群产生的DMSP浓度显著高于沉积物QY01 (50−55 cm)。贻贝足富集后菌群产生的DMSP浓度显著高于内脏团和鳃富集后菌群产生的DMSP浓度。高盐低氮MBM+l-Met混合培养基的13瓶富集培养样品来源于冷泉水体、沉积物、潜铠虾、贻贝以及热液区水体。其中热液区水体Hot1 (底层水)富集后菌群产生的DMSP浓度最高，为45.6 μmol/L。潜铠虾卵最低，为2.25 μmol/L。5瓶冷泉水体样品中，CTD03 (表层水)和ROV279 (距底40 m水)富集后菌群产生的DMSP浓度显著高于其余3瓶。总体上，高盐低氮MBM+l-Met混合培养基富集培养样品中菌群产生的DMSP浓度高于MBM+l-Met混合培养基，证实高盐低氮条件确实促进了细菌DMSP的合成过程^[29] (图1)。

2.2 富集培养获得的可培养细菌多样性

对南海F-冷泉和冲绳海槽Yaeyama Knoll热液区的水体、沉积物及动物样品进行了细菌的富集培养与分离纯化，共获得874株细菌。经16S rRNA基因测序鉴定，这874株细菌分属于4门6纲24目36科74属157种。门水平上(图2A)，变形菌门(Proteobacteria，557株)为主导类群，其次是厚壁菌门(Firmicutes，167株)、放线菌门(Actinobacteria，117株)和拟杆菌门(Bacteroidetes，33株)，分别占总分离菌株的64%、19%、13%和4%。纲水平上(图2B)，γ-变形菌纲(Gammaproteobacteria，447株)菌株最多，其次是芽孢杆菌纲(Bacilli，167株)、放线菌纲(Actinobacteria，117株)和α-变形菌纲(Alphaproteobacteria，103株)较多，分别占总分离菌株的51%、19%、13%和12%。黄杆菌纲(Flavobacteriia，33株)和β-变形菌纲(Betaproteobacteria，7株)菌株较少，分别占总分离菌株的4%和1%。属水平上(图2C)，γ-变形菌纲的海杆菌属(Marinobacter)菌株最多，共包括156株，占总分离菌株的18%，这些菌株分属于9个种；同为γ-变形菌纲的假单胞菌属(Pseudomonas)为第2大优势属，由10个不同的种组成，共79株细菌，占总分离菌株的9%。谷氨酸杆菌属(Glutamicibacter)、芽孢杆菌属(Bacillus)、海源菌属(Idiomarina)和假交替单胞菌属(Pseudoalteromonas)菌株也较多，分别包含2个种51株、7个种49株、5个种45株和5个种41株的细菌。此外，多个属仅包含1株可培养菌株，如小陌生菌属(Advenella)、农球菌属(Agrococcus)、农霉菌属(Agromyces)、短波单胞菌属(Brevundimonas)、棒杆菌属(Corynebacterium)、纤维芽孢杆菌属(Cytobacillus)、德沃斯氏菌属(Devosia)、亨里赛氏菌属(Henriciella)、海茎状菌属(Maricaulis)、海研站菌属(Mesonia)、鼠尾菌属(Muricauda)、涅斯捷连科氏菌属(Nesterenkonia)、类芽孢八叠球菌属(Paenisporosarcina)、副球菌属(Paracoccus)、海境芽孢杆菌属(Paraliobacillus)、假节杆菌属(Pseudarthrobacter)、盐水球菌属(Salinicoccus)、盐土芽孢杆菌属(Saliterribacillus)、斯塔普氏菌属(Stappia)和萨克利夫氏菌属(Sutcliffiella)。以上研究结果表明，南海F-冷泉和冲绳海槽Yaeyama Knoll热液区的水体、沉积物及动物样品富集培养获得的可培养细菌具有丰富的多样性。

2.3 不同培养基和样品中可培养细菌的多样性

经MBM+l-Met混合培养基、高盐低氮MBM+l-Met混合培养基、MBM+DMSP混合培养基富集培养后分离获得的可培养细菌菌株分别为103株、210株、561株。门水平上，变形菌门占绝对优势(57%−79%)。厚壁菌门和放线菌门在MBM+DMSP混合培养基中所占比例较高，分别为23%和16%。拟杆菌门在3种培养基中所占比例最低(2%−8%) (图3A)。在纲水平上，MBM+DMSP混合培养基中的可培养菌株来自γ-变形菌纲、芽孢杆菌纲、放线菌纲、α-变形菌纲、黄杆菌纲和β-变形菌纲6个纲，其余2种培养基均缺少β-变形菌纲的菌株，γ-变形菌纲在3种培养基中均占绝对优势(图3B)。在属和种水平上，经3种培养基富集培养后分离获得的细菌多样性由高到低依次为MBM+DMSP混合培养基(65属120种)、高盐低氮MBM+l-Met混合培养基(29属54种)、MBM+l-Met混合培养基(20属31种) (图3C)。

MBM+l-Met混合培养基的7瓶富集培养样品均来源于冷泉。其中，海杆菌属菌株最多，共包括33株，分属于5个种，占总分离菌株的32.0%，在水体、表层沉积物和贻贝鳃中均有分布。假单胞菌属为第2大优势属，共包括10株，分属于4个种，占细菌分离总数的9.7%，在表层沉积物和贻贝鳃中均有分布。另外中华微菌属(Sinomicrobium，8株1个种)、海源菌属(7株2个种)、近海螺旋菌属(Thalassospira，7株1个种)和谷氨酸杆菌属(6株1个种)获得的菌株也较多，其中中华微菌属仅分布于深层沉积物，海源菌属在沉积物和贻贝内脏团中均有分布，近海螺旋菌属仅分布于底层水体，谷氨酸杆菌属仅分布于贻贝内脏团。所有样品中贻贝内脏团包括的可培养细菌多样性最高(7个属)，ROV279 (距底5 m水)包括的可培养细菌菌株最多(25株)，而贻贝足菌株最少(4株) (图4)。

高盐低氮MBM+l-Met混合培养基的富集培养样品中，12瓶来源于冷泉，1瓶来源于热液区。从这些样品中总计分离获得210株菌，189株来源于冷泉样品，21株来源于热液区样品。海杆菌属菌株最多，共包括39株，分属于6个种，占总分离菌株的18.6%，在冷泉水体、动物和热液区水体来源的样品中均有分布。海源菌属为第2大优势属，共包括25株，分属于4个种，占总分离菌株的11.9%，在冷泉水体、沉积物和动物样品中均有分布。其次是假单胞菌属(21株3个种)、食烷菌属(Alcanivorax，17株1个种)和盐单胞菌属(Halomonas，17株3个种)，其中假单胞菌属仅分布于动物样品。海研站菌属和鼠尾菌属为热液区水体Hot1 (底层水)特有属。所有样品中冷泉水体ROV279 (距底5 m水)、潜铠虾刚毛和热液区水体Hot1 (底层水)包括的可培养细菌多样性最高(8个属)，潜铠虾卵包括的可培养细菌多样性最低(2个属)。潜铠虾刚毛和热液区水体Hot1 (底层水)包括的可培养细菌菌株最多(21株)，而冷泉水体ROV278 (底层水)菌株最少(8株) (图5)。

MBM+DMSP混合培养基的富集培养样品中，36瓶来源于冷泉，8瓶来源于热液区。这些样品中总计分离获得561株菌，489株来源于冷泉样品，72株来源于热液区样品。海杆菌属菌株最多，共包括84株，分属于6个物种，占总分离菌株的15.0%，在冷泉水体、沉积物、动物和热液区水体、沉积物样品中均有分布。其次是假单胞菌属(47株6种)、谷氨酸杆菌属(44株2种)和芽孢杆菌属(43株5种)菌株较多，其中假单胞菌属和芽孢杆菌属仅分布于冷泉水体、沉积物和动物样品，而谷氨酸杆菌属在冷泉水体、沉积物、动物和热液区沉积物样品中均有分布。交替单胞菌属(Alteromonas)和希瓦氏菌属(Shewanella)为热液区特有属。所有样品中，冷泉沉积物ROV277 (0−2 cm)的可培养细菌多样性最高(17个属)且菌株最多(45株)，冷泉沉积物ROV277 (6−8 cm)、贻贝外套膜和热液区沉积物HZ04 (40−45 cm)的可培养细菌多样性最低(均只有1个属)，其中冷泉沉积物ROV277 (6−8 cm)中分离得到的菌株最少(仅1株)。总体上，冷泉和热液区不同深度水体、沉积物和动物样品中可培养细菌的菌株数量和多样性有很大差别，冷泉沉积物样品可培养细菌种类和数量最多(85种，312株)，其次是冷泉水体(33种，101株)、潜铠虾(18种，49株)和热液区沉积物(17种，45株)，热液区水体(10种，27株)和贻贝(8种，27株)样品中可培养细菌种类和数量相对较少(图6)。

2.4 DMSP合成细菌多样性及其合成基因鉴定

从MBM+l-Met混合培养基富集培养样品分离获得的细菌中选取56株进行DMSP合成能力检测，其中8株具有DMSP合成能力，占被检测菌株的14.3%，分属于2个门(变形菌门和拟杆菌门)、3个纲(γ-变形菌纲4株、α-变形菌纲3株、黄杆菌纲1株)、6个属和6个种。在属水平上，具有DMSP合成能力的8株细菌包括交替单胞菌属和近海螺旋菌属各2株，海源菌属、中华微菌属、假栖大洋菌属(Pseudooceanicola)和弧菌属(Vibrio)各1株。其中，来源于冷泉水体的α-变形菌纲细菌海假栖大洋菌(Pseudooceanicola marinus) LXJ108 DMSP合成能力较强，合成量达到8.23 nmol (表3)。

从高盐低氮MBM+l-Met混合培养基富集培养样品分离获得的细菌中选取75株进行DMSP合成能力检测，其中7株(冷泉6株，热液区1株)具有DMSP合成能力，占被检测菌株的9.3%，均属于变形菌门，其中α-变形菌纲4株，γ-变形菌纲3株。在属水平上，具有DMSP合成能力的7株细菌包括近海螺旋菌属3株，交替单胞菌属、假交替单胞菌属、海源菌属和假栖大洋菌属各1株。其中α-变形菌纲的海假栖大洋菌(Pseudooceanicola marinus) LXJ117和深层近海螺旋菌(Thalassospira profundimaris) LXJ021、LXJ027 DMSP合成能力较强，分别来源于潜铠虾刚毛和冷泉水体(表4)。

总体上，冷泉和热液区中可培养DMSP合成细菌占比和多样性均较低，以α-变形菌纲和γ-变形菌纲为主。简并PCR结果表明，7株菌中含有已知的DMSP合成基因，2株含有dsyB，5株含有mmtN，其余菌株中未发现已知的DMSP合成基因，因此这些菌株可能含有潜在的新型DMSP合成基因(表3、表4)。

2.5 DMSP降解细菌多样性及其降解基因鉴定

从MBM+DMSP混合培养基富集培养样品分离获得的细菌中选取266株(冷泉233株，热液33株)进行DMSP降解能力检测，其中148株(冷泉130株，热液区18株)具有DMSP降解活性，占被检测菌株的55.6%，分属于4门6纲(γ-变形菌纲53株、放线菌纲48株、芽孢杆菌纲26株、α-变形菌纲17株、β-变形菌纲2株和黄杆菌纲2株) 19目27科40属71种。属水平上，谷氨酸杆菌属为冷泉样品中的第一优势属，共包括24株，分属于2个物种，占冷泉DMSP降解菌株的18.5%，在冷泉水体、沉积物和动物中均有分布；热液区DMSP降解菌株中不同属的数量相差不大，海杆菌属菌株数量最多(4株)，在热液区水体和沉积物中均有分布，希瓦氏菌属为热液区特有的DMSP降解类群。冷泉沉积物ROV277 (0−2 cm)中DMSP降解细菌多样性最高(14个属)且菌株数量最多(16株)。冷泉和热液区不同深度水体、沉积物和动物样品中DMSP降解细菌数量和多样性有很大差别，冷泉沉积物中DMSP降解菌种类和数量最多(49个种，78株)，其次是冷泉水体(17个种，24株)、潜铠虾(13个种，16株)、贻贝(6个种，12株)、热液区水体(8个种，10株)和热液区沉积物(7个种，8株) (图7)。

在148株DMSP降解细菌中，19株可通过裂解和脱甲基2种途径降解DMSP产生DMS和MeSH，127株仅能通过裂解途径产生DMS，2株仅能通过脱甲基途径产生MeSH。可通过裂解途径降解DMSP的菌株共计146株，远多于能通过脱甲基途径降解DMSP的菌株(21株)，表明冷泉和热液区的DMSP降解细菌可能主要通过裂解途径降解DMSP。在146株DMSP裂解菌中，有55株活性较强，产生DMS的速率超过0.10 nmol/h，其中放线菌纲28株、α-变形菌纲10株、γ-变形菌纲10株、芽孢杆菌纲7株，属水平上谷氨酸杆菌属的菌株最多(17株)，表明谷氨酸杆菌属可能是冷泉中介导DMSP裂解的主要类群(表5)。简并PCR结果表明，DMSP降解菌株中有2株(海源菌属)含有dddD^[47]，2株(海源菌属和亚硫酸盐杆菌属)含有dddL^[41]，5株(海源菌属、海杆菌属和假交替单胞菌属)含有dddX^[48]，3株(海源菌属和假单胞菌属)含有dmdA(C2)^[58]，未检测到dddP^[42]和dmdA (A1、A2、B3、D1、E2)^[58]，其余菌株中未发现已知的DMSP降解基因，可能含有潜在的新型DMSP降解基因。

3 讨论与结论

收起

DMSP的合成与降解是海洋中碳、硫元素循环的重要环节，对于多种海洋生物有重要的生理意义。尽管宏基因组学等非培养方法已广泛应用于DMSP合成与降解细菌的研究，但仍需要与纯培养方法相结合，从而发掘和鉴定潜在的新型DMSP合成与降解细菌。本研究对南海F-冷泉和冲绳海槽Yaeyama Knoll热液区的DMSP合成与降解细菌进行了富集培养和分离鉴定，探究了这2种特殊海洋环境中可培养的DMSP合成与降解细菌的多样性，并发现了潜在的新型DMSP代谢细菌。

本研究利用3种富集培养基对来自南海F-冷泉和冲绳海槽Yaeyama Knoll热液区多个站位的水体、沉积物和动物样品进行了富集培养，随后利用2216E培养基共分离纯化出874株菌。样品富集培养后分离获得的可培养细菌以变形菌门为优势类群，其余为厚壁菌门、放线菌门和拟杆菌门，纲水平为γ-变形菌纲占主导，这与此前海洋环境的可培养细菌研究得到的结论一致^[59-61]。属水平上，海杆菌属菌株最多，而周田田^[62]对F-冷泉样品的分菌结果为弧菌属占绝对优势，杨硕等^[63]在F-冷泉沉积物中分离的细菌以芽孢杆菌属为主。周田田^[62]只使用了MBM+l-Met混合培养基和MBM+DMSP混合培养基在16 ℃条件下进行富集培养，后续利用2216E培养基在28 ℃条件下进行分离培养；杨硕等^[63]将部分样品直接稀释涂布于R2A培养基并在28 ℃条件下分离培养，另一部分样品先使用2216E液体培养基在28 ℃下富集培养，后续使用2216E固体培养基在28 ℃条件下进行分离培养。样品来源、培养基和培养条件等因素的区别，可能是导致所分离菌株类群存在差异的主要原因。

经MBM+DMSP混合培养基富集培养后分离获得的细菌种类和数量(561株，120个种)远高于高盐低氮MBM+l-Met混合培养基(210株，54个种)和MBM+l-Met混合培养基获得的数量(103株，31个种)。这主要是因为DMSP可作为细菌的碳源和硫源，所以在培养基中添加DMSP能提高所获得细菌的多样性和数量。相比之下，高盐低氮MBM+l-Met混合培养基富集后细菌种类和数量远高于MBM+l-Met混合培养基，这可能是由于高盐低氮条件促进了DMSP的合成，影响了能够利用DMSP的细菌生长和繁殖。门水平上，经3种不同培养基富集培养后分离得到的细菌均以变形菌门占绝对优势，拟杆菌门占比均最低。纲水平上，γ-变形菌纲均占绝对优势，β-变形菌纲只存在于MBM+DMSP混合培养基中且占比最低。属水平上，海杆菌属菌株在不同的富集培养基中均为优势属，且广泛分布于冷泉水体、沉积物、动物和热液区水体、沉积物样品中，推测其物种有极强的环境适应性。假单胞菌属也占优势但只分布于冷泉各样品中，说明其物种适应冷泉环境而非热液区环境。值得注意的是，谷氨酸杆菌属在MBM+DMSP混合培养基中为优势属，可能与其能够利用DMSP有关。

在2种DMSP合成富集条件下，富集培养后DMSP浓度升高的样品都占少数，其中高盐低氮MBM+l-Met混合培养基DMSP浓度升高的样品瓶数多于MBM+l-Met混合培养基，说明高盐低氮条件的确能够促进细菌DMSP合成^[29]。进一步检测代表性菌株的DMSP合成能力，DMSP合成细菌在分离得到的可培养细菌中占比较低，且多数合成能力较弱。α-变形菌纲和γ-变形菌纲菌株为主要的DMSP合成类群，这与Liu等^[51]、Zhang等^[52]和高雪雨等^[53]的研究结果一致。Liu等^[51]在中国东海水体和沉积物中所分离的DMSP合成细菌以α-变形菌纲为主，Zhang等^[52]和高雪雨等^[53]对中国南海沉积物、北极北欧海海水、南极菲尔德斯半岛海水和沉积物的研究发现，DMSP合成细菌较少且γ-变形菌纲为优势类群。另外值得注意的是，在检测代表菌株是否具有DMSP合成能力的过程中，发现有不少菌株具有合成DMS的能力，主要是海杆菌属，海杆菌属此前被认为具有DMSP合成活性，现在发现其能裂解l-Met产生MeSH，再将MeSH甲基化生成DMS^[64]。DMS的合成可能是冷泉和热液生态系统中比DMSP合成更为普遍的过程。

与DMSP合成细菌情况不同，具有DMSP降解活性的菌株在被检测的总菌株中的数量占比和多样性均较高，且超过1/3的菌株降解能力较强。其中具有DMSP裂解途径的菌株占比为54.9%，与中国东海水体中的DMSP裂解菌株比例(约42.0%)接近^[50]。在所有DMSP降解菌株中，具有DMSP裂解能力的菌株(146株)远多于具有DMSP脱甲基能力的菌株(21株)。刘骥^[50]对夏季东海的研究和赵秀秀^[65]对马里亚纳海沟的研究也发现，DMSP裂解细菌比DMSP脱甲基细菌数量多。然而，Howard等^[66]研究发现海洋表层水体中能够通过脱甲基途径降解DMSP的细菌占细菌总数的一半以上。在纲水平上，冷泉来源的DMSP降解菌以放线菌纲和γ-变形菌纲为主，热液区来源的DMSP降解菌以γ-变形菌纲为主，林钰等^[61]和高雪雨等^[53]也发现γ-变形菌纲细菌是马里亚纳海沟沉积物和南、北极环境DMSP降解菌的主要类群。值得一提的是，放线菌纲的谷氨酸杆菌属为本研究发现的新型DMSP降解类群，在冷泉和热液区广泛分布。不同水体、沉积物和动物样品中DMSP降解类群差异很大，其中冷泉沉积物DMSP降解菌的数量和种类远高于其余样品，DMSP的降解可能对不少冷泉沉积物中的细菌有重要的生理意义。

本研究对冷泉和热液区这2个化能生态系统不同深度水体、沉积物以及动物中DMSP合成与降解细菌及相关基因进行了发掘与分析，拓展了对自然界DMSP合成与降解细菌多样性的认识，为进一步了解参与全球DMSP/DMS循环的海洋微生物提供了基础资料，同时为寻找新型DMSP合成与降解途径/基因提供了菌株资源。

基金

收起

中央高校基本科研业务费专项资金(202172002)
国家自然科学基金(42306115)
山东省自然科学基金(ZR2023QD017)
中国博士后科学基金(2022M722975)
山东省博士后创新项目(SDCX-ZG-202201016)

参考文献

收起

文献

收起

参考文献引证文献

排序方式：

[1]

BOETIUS A, WENZHÖFER F.Seafloor oxygen consumption fuelled by methane from cold seeps[J].Nature Geoscience,2013,6: 725-734.

https://doi.org/10.1038/ngeo1926

[2]

SUESS E.Marine cold seeps and their manifestations: geological control, biogeochemical criteria and environmental conditions[J].International Journal of Earth Sciences,2014,103(7):1889-1916.

https://doi.org/10.1007/s00531-014-1010-0

[3]

MACHIYAMA H, LIN S, FUJIKURA K, HUANG C, KU C, LIN L, LIU C, MORITA S, NUNOURA T, SOH W, TOKI T, YANG TF. Discovery of "Hydrothermal" chemosynthetic community in a cold seep environment, Taiwan Ridge: seafloor observation results from first rov cruise, off southwestern Taiwan[C]//AGU Fall Meeting Abstracts, US: American Geophysical Union, 2007: OS23A-1041.

[4]

LIN S, LIM Y, LIU C, YANG TF, CHEN YG, MACHIYAMA H, SOH W, FUJIKURA K.Taiwan Ridge, a cold seep with densely populated chemosynthetic community in the passive margin, southwest of Taiwan[J].Geochimica et Cosmochimica Acta,2007,71: 582.

[5]

LIN S, MACHIYAMA H, CHEN Y, SOH W, YANG T, WANG Y, LIM Y. Near sea floor gas hydrate formation and influence on pore water chemistry and authigenic carbonate at the Taiwan Ridge, South China sea[C]//AGU Fall Meeting Abstracts, US: American Geophysical Union, 2007: OS21A-05.

[6]

WANG XD, GUAN HX, QIU JW, XU T, PECKMANN J, CHEN DF, FENG D.Macro-ecology of cold seeps in the South China Sea[J].Geosystems and Geoenvironment,2022,1(3):100081.

https://doi.org/10.1016/j.geogeo.2022.100081

[7]

TIVEY MK.How to build a black smoker chimney[J].Oceanus,1998,41(2):22-26.

[8]

BEAULIEU SE, BAKER ET, GERMAN CR, MAFFEI A.An authoritative global database for active submarine hydrothermal vent fields[J].Geochemistry, Geophysics, Geosystems,2013,14(11):4892-4905.

https://doi.org/10.1002/2013GC004998

[9]

MIYAZAKI J, KAWAGUCCI S, MAKABE A, TAKAHASHI A, KITADA K, TORIMOTO J, MATSUI Y, TASUMI E, SHIBUYA T, NAKAMURA K, HORAI S, SATO S, ISHIBASHI JI, KANZAKI H, NAKAGAWA S, HIRAI M, TAKAKI Y, OKINO K, WATANABE HK, KUMAGAI H, et al.Deepest and hottest hydrothermal activity in the Okinawa Trough: the Yokosuka site at Yaeyama Knoll[J].Royal Society Open Science,2017,4(12):171570.

https://doi.org/10.1098/rsos.171570

[10]

LEVIN LA, BACO AR, BOWDEN DA, COLACO A, CORDES EE, CUNHA MR, DEMOPOULOS AWJ, GOBIN J, GRUPE BM, LE J, METAXAS A, NETBURN AN, ROUSE GW, THURBER AR, TUNNICLIFFE V, van DOVER CL, VANREUSEL A, WATLING L.Hydrothermal vents and methane seeps: rethinking the sphere of influence[J].Frontiers in Marine Science,2016,3: 72.

[11]

KIENE RP, LINN LJ, BRUTON JA.New and important roles for DMSP in marine microbial communities[J].Journal of Sea Research,2000,43(3/4):209-224.

[12]

CHALLENGER F, SIMPSON MI.A precursor of the dimethyl sulphide evolved by Polysiphonia fastigiata; dimethyl-beta-propiothetine (dimethyl-beta- carboxythylsulphonium hydroxide) and its salts[J].Biochemical Journal,1947,41(3):xl.

[13]

ARCHER SD, WIDDICOMBE CE, TARRAN GA, REES AP, BURKILL PH.Production and turnover of particulate dimethylsulphoniopropionate during a coccolithophore bloom in the northern North Sea[J].Aquatic Microbial Ecology,2001,24: 225-241.

https://doi.org/10.3354/ame024225

[14]

HOWARD EC, HENRIKSEN JR, BUCHAN A, REISCH CR, BÜRGMANN H, WELSH R, YE WY, GONZÁLEZ JM, MACE K, JOYE SB, KIENE RP, WHITMAN WB, MORAN MA.Bacterial taxa that limit sulfur flux from the ocean[J].Science,2006,314(5799):649-652.

https://doi.org/10.1126/science.1130657

[15]

KIRST GO, THIEL C, WOLFF H, NOTHNAGEL J, WANZEK M, ULMKE R.Dimethylsulfoniopropionate (DMSP) in icealgae and its possible biological role[J].Marine Chemistry,1991,35(1/2/3/4):381-388.

[16]

ZHENG YF, WANG JY, ZHOU S, ZHANG YH, LIU J, XUE CX, WILLIAMS BT, ZHAO XX, ZHAO L, ZHU XY, SUN C, ZHANG HH, XIAO T, YANG GP, TODD JD, ZHANG XH.Bacteria are important dimethylsulfoniopropionate producers in marine aphotic and high-pressure environments[J].Nature Communications,2020,11(1):4658.

https://doi.org/10.1038/s41467-020-18434-4

[17]

SUNDA W, KIEBER DJ, KIENE RP, HUNTSMAN S.An antioxidant function for DMSP and DMS in marine algae[J].Nature,2002,418(6895):317-320.

https://doi.org/10.1038/nature00851

[18]

KARSTEN U, KÜCK K, VOGT C, KIRST GO.Dimethylsulfoniopropionate production in phototrophic organisms and its physiological functions as a cryoprotectant//KIENE RP, VISSCHER PT, KELLER MD, KIRST GO[J].Biological and Environmental Chemistry of DMSP and Related Sulfonium Compounds. Boston. MA: Springer US,1996: 143-153.

[19]

WOLFE GV, STEINKE M, KIRST GO.Grazing-activated chemical defence in a unicellular marine alga[J].Nature,1997,387: 894-897.

https://doi.org/10.1038/43168

[20]

JOHNSON WM, KIDO SOULE MC, KUJAWINSKI EB.Evidence for quorum sensing and differential metabolite production by a marine bacterium in response to DMSP[J].The ISME Journal,2016,10(9):2304-2316.

https://doi.org/10.1038/ismej.2016.6

[21]

TROTTMANN F, ISHIDA K, FRANKE J, STANIŠIĆ A, ISHIDA-ITO M, KRIES H, POHNERT G, HERTWECK C.Sulfonium acids loaded onto an unusual thiotemplate assembly line construct the cyclopropanol warhead of a Burkholderia virulence factor[J].Angewandte Chemie International Edition,2020,59(32):13511-13515.

https://doi.org/10.1002/anie.202003958

[22]

CHARLSON RJ, LOVELOCK JE, ANDREAE MO, WARREN SG.Oceanic phytoplankton, atmospheric sulphur, cloud albedo and climate[J].Nature,1987,326: 655-661.

https://doi.org/10.1038/326655a0

[23]

KELLER MD, BELLOWS WK, GUILLARD RRL.Dimethylsulfide production and marine phytoplankton: an additional impact of unusual blooms//Novel Phytoplankton Blooms[J].Berlin, Heidelberg: Springer Berlin Heidelberg,1989: 101-115.

[24]

EDWARDS DM, REED RH, CHUDEK JA, FOSTER R, STEWART WDP.Organic solute accumulation in osmotically-stressed Enteromorpha intestinalis[J].Marine Biology,1987,95(4):583-592.

https://doi.org/10.1007/BF00393102

[25]

RAINA JB, TAPIOLAS DM, FORÊT S, LUTZ A, ABREGO D, CEH J, SENECA FO, CLODE PL, BOURNE DG, WILLIS BL, MOTTI CA.DMSP biosynthesis by an animal and its role in coral thermal stress response[J].Nature,2013,502(7473):677-680.

https://doi.org/10.1038/nature12677

[26]

PAQUET L, RATHINASABAPATHI B, SAINI H, ZAMIR L, DA GG, HUANG ZH, HANSON AD.Accumulation of the compatible solute 3-dimethylsulfoniopropionate in sugarcane and its relatives, but not other gramineous crops[J].Functional Plant Biology,1994,21(1):37.

https://doi.org/10.1071/PP9940037

[27]

JAMES F, PAQUET L, SPARACE SA, GAGE DA, HANSON AD.Evidence implicating dimethylsulfoniopropionaldehyde as an intermediate in dimethylsulfoniopropionate biosynthesis[J].Plant Physiology,1995,108(4):1439-1448.

https://doi.org/10.1104/pp.108.4.1439

[28]

KOCSIS MG, NOLTE KD, RHODES D, SHEN TL, GAGE DA, HANSON AD.Dimethylsulfoniopropionate biosynthesis in Spartina alterniflora1. evidence that S-methylmethionine and dimethylsulfoniopropylamine are intermediates[J].Plant Physiology,1998,117(1):273-281.

https://doi.org/10.1104/pp.117.1.273

[29]

CURSON ARJ, LIU J, BERMEJO MARTÍNEZ A, GREEN RT, CHAN Y, CARRIÓN O, WILLIAMS BT, ZHANG SH, YANG GP, BULMAN PAGE PC, ZHANG XH, TODD JD.Dimethylsulfoniopropionate biosynthesis in marine bacteria and identification of the key gene in this process[J].Nature Microbiology,2017,2: 17009.

[30]

GAGE DA, RHODES D, NOLTE KD, HICKS WA, LEUSTEK T, COOPER AJ, HANSON AD.A new route for synthesis of dimethylsulphoniopropionate in marine algae[J].Nature,1997,387(6636):891-894.

[31]

UCHIDA A, OOGURI T, ISHIDA T, ISHIDA Y.Incorporation of methionine into dimethylthiopropanoic acid in the dinoflagellate Crypthecodinium cohnii[J].Nippon Suisan Gakkaishi,1993,59(5):851-855.

[32]

CURSON ARJ, WILLIAMS BT, PINCHBECK BJ, SIMS LP, MARTÍNEZ AB, RIVERA PPL, KUMARESAN D, MERCADÉ E, SPURGIN LG, CARRIÓN O, MOXON S, CATTOLICO RA, KUZHIUMPARAMBIL U, GUAGLIARDO P, CLODE PL, RAINA JB, TODD JD.DSYB catalyses the key step of dimethylsulfoniopropionate biosynthesis in many phytoplankton[J].Nature Microbiology,2018,3(4):430-439.

[33]

KAGEYAMA H, TANAKA Y, SHIBATA A, WADITEE-SIRISATTHA R, TAKABE T.Dimethylsulfoniopropionate biosynthesis in a diatom Thalassiosira pseudonana: identification of a gene encoding MTHB-methyltransferase[J].Archives of Biochemistry and Biophysics,2018,645: 100-106.

[34]

WILLIAMS BT, COWLES K, MARTÍNEZ AB, CURSON ARJ, ZHENG YF, LIU JL, NEWTON-PAYNE S, HIND AJ, LI CY, RIVERA PPL, CARRIÓN O, LIU J, SPURGIN LG, BREARLEY CA, MACKENZIE BW, PINCHBECK BJ, PENG M, PRATSCHER J, ZHANG XH, ZHANG YZ, MURRELL JC, TODD JD.Bacteria are important dimethylsulfoniopropionate producers in coastal sediments[J].Nature Microbiology,2019,4(11):1815-1825.

[35]

WANG JY, CURSON ARJ, ZHOU S, CARRIÓN O, LIU J, VIEIRA AR, WALSHAM KS, MONACO S, LI CY, DONG QY, WANG Y, RIVERA PPL, WANG XD, ZHANG M, HANWELL L, WALLACE M, ZHU XY, LEÃO PN, LEA-SMITH DJ, ZHANG YZ, ZHANG XH, TODD JD.Alternative dimethylsulfoniopropionate biosynthesis enzymes in diverse and abundant microorganisms[J].Nature Microbiology,2024,9(8):1979-1992.

[36]

CURSON ARJ, TODD JD, SULLIVAN MJ, JOHNSTON AWB.Catabolism of dimethylsulphoniopropionate: microorganisms, enzymes and genes[J].Nature Reviews Microbiology,2011,9(12):849-859.

[37]

REISCH CR, MORAN MA, WHITMAN WB.Bacterial catabolism of dimethylsulfoniopropionate (DMSP)[J].Frontiers in Microbiology,2011,2: 172.

[38]

REISCH CR, STOUDEMAYER MJ, VARALJAY VA, AMSTER IJ, MORAN MA, WHITMAN WB.Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria[J].Nature,2011,473(7346):208-211.

[39]

YOCH DC.Dimethylsulfoniopropionate: its sources, role in the marine food web, and biological degradation to dimethylsulfide[J].Applied and Environmental Microbiology,2002,68(12):5804-5815.

[40]

THUME K, GEBSER B, CHEN L, MEYER N, KIEBER DJ, POHNERT G.The metabolite dimethylsulfoxonium propionate extends the marine organosulfur cycle[J].Nature,2018,563(7731):412-415.

[41]

CURSON ARJ, ROGERS R, TODD JD, BREARLEY CA, JOHNSTON AWB.Molecular genetic analysis of a dimethylsulfoniopropionate lyase that liberates the climate-changing gas dimethylsulfide in several marine alpha-proteobacteria and Rhodobacter sphaeroides[J].Environmental Microbiology,2008,10(3):757-767.

[42]

TODD JD, CURSON ARJ, DUPONT CL, NICHOLSON P, JOHNSTON AWB.The dddP gene, encoding a novel enzyme that converts dimethylsulfoniopropionate into dimethyl sulfide, is widespread in ocean metagenomes and marine bacteria and also occurs in some Ascomycete fungi[J].Environmental Microbiology,2009,11(6):1376-1385.

[43]

TODD JD, CURSON ARJ, KIRKWOOD M, SULLIVAN MJ, GREEN RT, JOHNSTON AWB.DddQ, a novel, cupin-containing, dimethylsulfoniopropionate lyase in marine roseobacters and in uncultured marine bacteria[J].Environmental Microbiology,2011,13(2):427-438.

[44]

TODD JD, KIRKWOOD M, NEWTON-PAYNE S, JOHNSTON AWB.DddW, a third DMSP lyase in a model Roseobacter marine bacterium, Ruegeria pomeroyi DSS-3[J].The ISME Journal,2012,6(1):223-226.

[45]

CURSON ARJ, SULLIVAN MJ, TODD JD, JOHNSTON AWB.DddY, a periplasmic dimethylsulfoniopropionate lyase found in taxonomically diverse species of Proteobacteria[J].The ISME Journal,2011,5(7):1191-1200.

[46]

SUN J, TODD JD, THRASH JC, QIAN YP, QIAN MC, TEMPERTON B, GUO JZ, FOWLER EK, ALDRICH JT, NICORA CD, LIPTON MS, SMITH RD, de LEENHEER P, PAYNE SH, JOHNSTON AWB, DAVIE-MARTIN CL, HALSEY KH, GIOVANNONI SJ.The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol[J].Nature Microbiology,2016,1(8):16065.

[47]

TODD JD, ROGERS R, LI YG, WEXLER M, BOND PL, SUN L, CURSON ARJ, MALIN G, STEINKE M, JOHNSTON AWB.Structural and regulatory genes required to make the gas dimethyl sulfide in bacteria[J].Science,2007,315(5812):666-669.

[48]

LI CY, WANG XJ, CHEN XL, SHENG Q, ZHANG S, WANG P, QUARESHY M, RIHTMAN B, SHAO X, GAO C, LI FC, LI SY, ZHANG WP, ZHANG XH, YANG GP, TODD JD, CHEN Y, ZHANG YZ.A novel ATP dependent dimethylsulfoniopropionate lyase in bacteria that releases dimethyl sulfide and acryloyl-CoA[J].eLife,2021,10: e64045.

[49]

WANG SY, ZHANG N, TENG ZJ, WANG XD, TODD JD, ZHANG YZ, CAO HY, LI CY.A new dimethylsulfoniopropionate lyase of the cupin superfamily in marine bacteria[J].Environmental Microbiology,2023,25(7):1238-1249.

[50]

刘骥. 中国东海DMSP分解和合成代谢细菌多样性及典型菌株相关功能基因研究[D]. 青岛: 中国海洋大学博士学位论文, 2018.

LIU J. Diversity of DMSP-decomposing and anabolic bacteria and related functional genes of typical strains in the East China Sea of China[D]. Qingdao: Doctoral Dissertation of Ocean University of China, 2018 (in Chinese).

[51]

LIU J, ZHANG YH, LIU JL, ZHONG HH, WILLIAMS BT, ZHENG YF, CURSON ARJ, SUN C, SUN H, SONG DL, WAGNER MACKENZIE B, BERMEJO MARTÍNEZ A, TODD JD, ZHANG XH.Bacterial dimethylsulfoniopropionate biosynthesis in the East China Sea[J].Microorganisms,2021,9(3):657.

[52]

ZHANG YH, SUN K, SUN C, SHI XC, TODD JD, ZHANG XH.Dimethylsulfoniopropionate biosynthetic bacteria in the subseafloor sediments of the South China Sea[J].Frontiers in Microbiology,2021,12: 731524.

[53]

高雪雨, 商丽, 吴蕾蕾, 张晓华, 史晓翀.参与DMSP/DMS循环的极地细菌初步筛选及其多样性研究[J]. 中国海洋大学学报(自然科学版),2022,52(9):61-70.

GAO XY, SHANG L, WU LL, ZHANG XH, SHI XC.Preliminary screening of polar bacteria participating in DMSP/DMS cycle and the diversity analysis[J].Periodical of Ocean University of China,2022,52(9):61-70 (in Chinese).

[54]

张晓华, 刘吉文, 于敏, 战渊超, 史晓翀, 莫照兰, 张蕴慧, 王晓磊, 杨世民, 李伟, 高风, 于淑贤, 李静, 张钰琳, 何新新, 王金燕, 冉凌蔓, 刘荣华, 翟欣奕, 顾冰玉, 等.海洋微生物学[J]. 3版. 北京: 科学出版社,2024: 1-496.

ZHANG XH, LIU JW, YU M, ZHAN YC, SHI XC, MO ZL, ZHANG YH, WANG XL, YANG SM, LI W, GAO F, YU SX, LI J, ZHANG YL, HE XX, WANG JY, RAN LM, LIU RH, ZHAI XY, GU BY, et al.Marine Microliology[J]. 3rd Edition. Beijing: Science Press,2024: 1-496 (in Chinese).

[55]

MOORE E, ARNSCHEIDT A, KRÜGER A, STRÖMPL C, MAU M.Section 1 update: simplified protocols for the preparation of genomic DNA from bacterial cultures//Molecular Microbial Ecology Manual[J].Dordrecht: Springer Netherlands,2008: 1905-1919.

[56]

WEISBURG WG, BARNS SM, PELLETIER DA, LANE DJ.16S ribosomal DNA amplification for phylogenetic study[J]. Journal of Bacteriology,1991,173(2):697-703.

[57]

RAINA JB, TAPIOLAS D, WILLIS BL, BOURNE DG.Coral-associated bacteria and their role in the biogeochemical cycling of sulfur[J].Applied and Environmental Microbiology,2009,75(11):3492-3501.

[58]

VARALJAY VA, HOWARD EC, SUN SL, MORAN MA.Deep sequencing of a dimethylsulfoniopropionate- degrading gene (dmdA) by using PCR primer pairs designed on the basis of marine metagenomic data[J].Applied and Environmental Microbiology,2010,76(2):609-617.

[59]

商丽, 史晓翀, 王晓宇, 张晓华.北欧海海水可培养细菌多样性[J]. 微生物学报,2017,57(9):1323-1331. https://actamicro.ijournals.cn/actamicrocn/article/abstract/20170903?st=search

SHANG L, SHI XC, WANG XY, ZHANG XH.Diversity of culturable bacterial in the surface seawater of the Nordic Sea[J].Acta Microbiologica Sinica,2017,57(9):1323-1331 (in Chinese). https://actamicro.ijournals.cn/actamicrocn/article/abstract/20170903?st=search

[60]

孙创, 王金燕, 张钰琳, 张蕴慧, 朱晓雨, 陈朝晖, 张晓华.利用改良培养基探究西太平洋海水可培养细菌多样性[J]. 微生物学报,2021,61(4):845-861. https://actamicro.ijournals.cn/actamicrocn/article/abstract/20210408?st=search

SUN C, WANG JY, ZHANG YL, ZHANG I, ZHU XY, CHEN HC, ZHANG XH.Exploring the diversity of cultivated bacteria in the Western Pacific waters through improved culture media[J].Acta Microbiologica Sinica,2021,61(4):845-861 (in Chinese). https://actamicro.ijournals.cn/actamicrocn/article/abstract/20210408?st=search

[61]

林钰, 刘荣华, 周顺, 朱晓雨, 王金燕, 张晓华.马里亚纳海沟沉积物可培养异养细菌的多样性及其DMSP降解能力[J]. 微生物学报,2021,61(4):828-844. https://actamicro.ijournals.cn/actamicrocn/article/abstract/20210407?st=search

LIN Y, LIU RH, ZHOU S, ZHU XY, WANG JY, ZHANG XH.Diversity of culturable heterotrophic bacteria from sediments of the Mariana Trench and their ability to degrade dimethylsulfoniopropionate (DMSP)[J].Acta Microbiologica Sinica,2021,61(4):828-844 (in Chinese). https://actamicro.ijournals.cn/actamicrocn/article/abstract/20210407?st=search

[62]

周田田. 南海F冷泉区DMSP降解与合成菌的筛选及弧菌中新型DMSP/l-Met降解基因的研究[D]. 青岛: 中国海洋大学硕士学位论文, 2024.

ZHOU TT. Screening of DMSP degrading and producing strains in F Cold Seep of the South China Sea and research on the new-type DMSP/l-Met degradation genes in vibrios[D]. Qingdao: Master's Thesis of Ocean University of China, 2024 (in Chinese).

[63]

杨硕, 高峥, 邵宗泽.南海冷泉区深海沉积物中细菌的分离培养及多样性分析[J]. 氨基酸和生物资源,2016,38(1):34-40.

YANG S, GAO Z, SHAO ZZ.Diversity of cultivable bacteria in deep sea sediments from cold seeps in the South China Sea[J].Amino Acids & Biotic Resources,2016,38(1):34-40.

[64]

ZHANG YH, SUN C, GUO ZH, LIU LY, ZHANG XT, SUN K, ZHENG YF, GATES AJ, TODD JD, ZHANG XH.An S-methyltransferase that produces the climate-active gas dimethylsulfide is widespread across diverse marine bacteria[J].Nature Microbiology,2024,9(10):2614-2625.

[65]

赵秀秀. 马里亚纳海沟异养细菌的分离培养、碳源利用及DMSP合成与降解能力研究[D]. 青岛: 中国海洋大学硕士学位论文, 2020.

ZHAO XX. Isolation, culture, carbon source utilization, DMSP synthesis and degradation ability of heterotrophic bacteria in Mariana Trench[D]. Qingdao: Master's Thesis of Ocean University of China, 2020 (in Chinese).

[66]

HOWARD EC, SUN SL, BIERS EJ, MORAN MA.Abundant and diverse bacteria involved in DMSP degradation in marine surface waters[J].Environmental Microbiology,2008,10(9):2397-2410.

2024年第64卷第12期

PDF下载

引用本文

BibTeX

文章信息

doi: 10.13343/j.cnki.wsxb.20240708

接收时间：2024-11-11
首发时间：2026-03-21
出版时间：2024-12-04

补充材料

相关文章

文章信息

作者

出版历史

收稿日期：2024-11-11
录用日期：2024-11-22

基金

Fundamental Research Funds for the Central Universities(202172002)

中央高校基本科研业务费专项资金(202172002)

National Natural Science Foundation of China(42306115)

国家自然科学基金(42306115)

Shandong Provincial Natural Science Foundation(ZR2023QD017)

山东省自然科学基金(ZR2023QD017)

China Postdoctoral Science Foundation(2022M722975)

中国博士后科学基金(2022M722975)

Postdoctoral Innovation Program of Shandong Province(SDCX-ZG-202201016)

山东省博士后创新项目(SDCX-ZG-202201016)

作者信息

1 中国海洋大学海洋生命学院, 山东青岛 266003

2 青岛海洋科学技术中心, 海洋生态与环境科学功能实验室, 山东青岛 266237

3 中国海洋大学, 深海圈层与地球系统前沿科学中心, 山东青岛 266100

4 中国海洋大学, 海洋生物多样性与进化研究所, 山东青岛 266003

通讯作者:

参考文献

分享链接

https://castjournals.cast.org.cn/joweb/wswxb/CN/10.13343/j.cnki.wsxb.20240708

分享至

全文二维码

扫描看全文

引用本文

BibTeX

本文的引用情况

2种不同金属材料的力学参数

科 Family	属数 Number of genus	种数 Number of species	占总种数比例 Percentage of total species (%)	属 Genus	种数 Number of species	占总种数比例 Percentage of total species (%)
鹅膏菌科Amanitaceae	2	11	5.26	鹅膏菌属 Amanita	10	4.78
小菇科 Mycenaceae	2	12	5.74	丝盖伞属 Inocybe	5	2.39
多孔菌科 Polyporaceae	8	14	6.70	蜡蘑属 Laccaria	5	2.39
红菇科 Russulaceae	3	23	11.00	小皮伞属 Marasmius	6	2.87
				小菇属 Mycena	11	5.26
				光柄菇属 Pluteus	5	2.39
				红菇属 Russula	17	8.13
				栓菌属 Trametes	5	2.39

关闭全屏

BibTeX
EndNote
RefWorks
TxT

Location	Station	Longitude	Latitude	Depth (m)	Sample collection section
F-cold seep	ROV272	119°17.142 9′	22°06.902 5′	1 127	Pushcore sediments (1−2 cm, 5−6 cm)
ROV272	119°17.142 9′	22°06.902 5′	1 127	Mussel (gill)
QY01	119°17.520 2′	22°06.499 6′	1 154	Gravity column sediments (0−5 cm, 5−10 cm, 50−55 cm)
CTD03	119°17.141 0′	22°06.932 0′	1 120	Surface water, 800 m water, bottom water
C2-	119°17.149 4′	22°06.894 0′	1 130	Gravity column sediments (0−5 cm, 120−125 cm, 235−240 cm)
C1	119°17.093 7′	22°06.965 8′	1 167	Gravity column sediments (0−3 cm, 54−57 cm, 105−108 cm)
ROV277	119°17.153 8′	22°06.925 4′	1 129	Shinkaia crosnieri (intestine, bristle and male gonad) Mussel (visceral mass, mantle and foot)
ROV277	119°17.140 6′	22°06.924 3′	1 124	Bottom water
ROV277	119°17.153 8′	22°06.904 2′	1 129	Pushcore sediments (0−2 cm, 6−8 cm, 8−10 cm)
ROV278	119°17.1615′	22°06.881 6′	1 135	Pushcore sediments (0−2 cm, 6−8 cm, 10−12 cm)
ROV278	119°17.157 9′	22°06.884 3′	1 135	Bottom water
ROV279	119°17.160 0′	22°06.920 5′	1 131	Pushcore sediments (0−2 cm, 6−8 cm)
ROV279	119°17.136 7′	22°06.927 6′	1 131	Polynoidae Tubeworm Shinkaia crosnieri (egg and gill)
ROV279	119°17.140 2′	22°06.925 2′	1 120	Water 5 m and 40 m from bottom
Yaeyama Knoll hydrothermal field	Hot1	124°22.382 0′	25°15.795 0′	2 157	1 000 m water, bottom water
RYSHW	124°22.366 9′	25°15.843 7′	2 157	Pushcore surface and bottom sediments
HZ04	124°22.363 2′	25°15.141 5′	2 279	Gravity column sediments (0−5 cm, 40−45 cm, 60−65 cm, 65−70 cm)

Location

Station

Longitude

Latitude

Depth (m)

Sample collection section

F-cold seep

ROV272

119°17.142 9′

22°06.902 5′

1 127

Pushcore sediments (1−2 cm, 5−6 cm)

ROV272

119°17.142 9′

22°06.902 5′

1 127

Mussel (gill)

QY01

119°17.520 2′

22°06.499 6′

1 154

Gravity column sediments (0−5 cm, 5−10 cm, 50−55 cm)

CTD03

119°17.141 0′

22°06.932 0′

1 120

Surface water, 800 m water, bottom water

C2-

119°17.149 4′

22°06.894 0′

1 130

Gravity column sediments (0−5 cm, 120−125 cm, 235−240 cm)

119°17.093 7′

22°06.965 8′

1 167

Gravity column sediments (0−3 cm, 54−57 cm, 105−108 cm)

ROV277

119°17.153 8′

22°06.925 4′

1 129

Shinkaia crosnieri (intestine, bristle and male gonad)
Mussel (visceral mass, mantle and foot)

ROV277

119°17.140 6′

22°06.924 3′

1 124

Bottom water

ROV277

119°17.153 8′

22°06.904 2′

1 129

Pushcore sediments (0−2 cm, 6−8 cm, 8−10 cm)

ROV278

119°17.1615′

22°06.881 6′

1 135

Pushcore sediments (0−2 cm, 6−8 cm, 10−12 cm)

ROV278

119°17.157 9′

22°06.884 3′

1 135

Bottom water

ROV279

119°17.160 0′

22°06.920 5′

1 131

Pushcore sediments (0−2 cm, 6−8 cm)

ROV279

119°17.136 7′

22°06.927 6′

1 131

Polynoidae
Tubeworm
Shinkaia crosnieri (egg and gill)

ROV279

119°17.140 2′

22°06.925 2′

1 120

Water 5 m and 40 m from bottom

Yaeyama Knoll hydrothermal field

Hot1

124°22.382 0′

25°15.795 0′

2 157

1 000 m water, bottom water

RYSHW

124°22.366 9′

25°15.843 7′

2 157

Pushcore surface and bottom sediments

HZ04

124°22.363 2′

25°15.141 5′

2 279

Gravity column sediments (0−5 cm, 40−45 cm, 60−65 cm, 65−70 cm)

Target genes	Primers name	Oligonucleotide (5′→3′)	Annealing temperature (℃)	References
dsyB	dsyB_F dsyB_R	CATGGGSTCSAAGGCSCTKTT GCAGRTARTCGCCGAAATCGTA	61	[29]
mmtN	mmtN_F mmtN_R	CCGAGGTGGTCATGAAYTTYGG GGATCACGCACACYTCRTGRTA	54	[34]
dddP	dddP_F dddP_R	AAYGAAATWGTTGCCTTTGA GCATDGCRTAAATCATATC	41	[42]
dddL	dddL_F dddL_R	CTGGGAATACGGCTACGAGA GTTCAAGATCAGCGATCCGG	53	[57]
dddD	dddD_F dddD_R	ACCAACGTCATTGCAGGACC TGTGCGTGTTCTTCCGGTG	56	[57]
dddX	dddX_F dddX_R	TTTGAAAACTCAGGCTTTTC TGAATATGGTAATGGTACTT	46	[48]
dmdA (A/1)	A/1_F A/1_R	ATGGTGATTTGCTTCAGTTTCT CCCTGCTTTGACCAACC	53	[58]
dmdA (A/2)	A/2_F A/2_R	CGATGAACATTGGTGGGTTTCTA GCCATTAGGTCGTCTGATTTTGG	59	[58]
dmdA (B/3)	B/3_F B/3_R	GATGTCTCCTGCCAACGTCAGGTCGA ACCGGGTCATTGATCATGCCTGCG	62	[58]
dmdA (C/2)	C/2_291F C/2_482R	AGATGAAAATGCTGGAATGATAAATG AAATCTTCAGACTTTGGACCTTG	50	[58]
dmdA (D/1)	D/1_268F D/1_356R	AGATGTTATTATTGTCCAATAATTGATG ATCCACCATCTATCTTCAGCTA	49	[58]
dmdA (E/2)	E/2_F E/2_R	CATGTTCAGATCTGGGACGT AGCGGCACATACATGCACT	57	[58]

Target genes

Primers name

Oligonucleotide (5′→3′)

Annealing temperature (℃)

References

dsyB

dsyB_F
dsyB_R

CATGGGSTCSAAGGCSCTKTT
GCAGRTARTCGCCGAAATCGTA

[29]

mmtN

mmtN_F
mmtN_R

CCGAGGTGGTCATGAAYTTYGG
GGATCACGCACACYTCRTGRTA

[34]

dddP

dddP_F
dddP_R

AAYGAAATWGTTGCCTTTGA
GCATDGCRTAAATCATATC

[42]

dddL

dddL_F
dddL_R

CTGGGAATACGGCTACGAGA
GTTCAAGATCAGCGATCCGG

[57]

dddD

dddD_F
dddD_R

ACCAACGTCATTGCAGGACC
TGTGCGTGTTCTTCCGGTG

[57]

dddX

dddX_F
dddX_R

TTTGAAAACTCAGGCTTTTC
TGAATATGGTAATGGTACTT

[48]

dmdA (A/1)

A/1_F
A/1_R

ATGGTGATTTGCTTCAGTTTCT
CCCTGCTTTGACCAACC

[58]

dmdA (A/2)

A/2_F
A/2_R

CGATGAACATTGGTGGGTTTCTA
GCCATTAGGTCGTCTGATTTTGG

[58]

dmdA (B/3)

B/3_F
B/3_R

GATGTCTCCTGCCAACGTCAGGTCGA
ACCGGGTCATTGATCATGCCTGCG

[58]

dmdA (C/2)

C/2_291F
C/2_482R

AGATGAAAATGCTGGAATGATAAATG
AAATCTTCAGACTTTGGACCTTG

[58]

dmdA (D/1)

D/1_268F
D/1_356R

AGATGTTATTATTGTCCAATAATTGATG
ATCCACCATCTATCTTCAGCTA

[58]

dmdA (E/2)

E/2_F
E/2_R

CATGTTCAGATCTGGGACGT
AGCGGCACATACATGCACT

[58]

Strain source	Strain number	Species	DMSP synthesis activity (nmol)	DMSP synthesis gene
ROV277 (bottom water)	LXJ078	Thalassospira profundimaris	0.75	mmtN^[34]
LXJ079	Thalassospira profundimaris	0.55	mmtN^[34]
QY01 (50−55 cm)	LXJ044	Sinomicrobium oceani	0.63
LXJ048	Idiomarina zobellii	0.57
Mussel (gill)	LXJ091	Alteromonas tagae	0.42
LXJ093	Alteromonas tagae	0.30
ROV279 (water 5 m from bottom)	LXJ106	Vibrio chagasii	0.73
LXJ108	Pseudooceanicola marinus	8.23	dsyB^[29]

Strain source

Strain number

Species

DMSP synthesis activity (nmol)

DMSP synthesis gene

ROV277
(bottom water)

LXJ078

Thalassospira profundimaris

0.75

mmtN^[34]

LXJ079

Thalassospira profundimaris

0.55

mmtN^[34]

QY01 (50−55 cm)

LXJ044

Sinomicrobium oceani

0.63

LXJ048

Idiomarina zobellii

0.57

Mussel (gill)

LXJ091

Alteromonas tagae

0.42

LXJ093

Alteromonas tagae

0.30

ROV279
(water 5 m from bottom)

LXJ106

Vibrio chagasii

0.73

LXJ108

Pseudooceanicola marinus

8.23

dsyB^[29]

Strain source	Strain number	Species	DMSP synthesis activity (nmol)	DMSP synthesis gene
Hot1 (bottom water)	LXJ035	Alteromonas macleodii	0.29
ROV279 (water 40 m from bottom)	LXJ021	Thalassospira profundimaris	1.84	mmtN^[34]
ROV277 (bottom water)	LXJ027	Thalassospira profundimaris	2.86	mmtN^[34]
ROV272 (5−6 cm)	LXJ008	Thalassospira profundimaris	0.30	mmtN^[34]
ROV277 (8−10 cm)	LXJ110	Idiomarina loihiensis	0.47
Shinkaia crosnieri (bristle)	LXJ113	Pseudoalteromonas shioyasakiensis	0.41
LXJ117	Pseudooceanicola marinus	3.18	dsyB^[29]

Strain source

Strain number

Species

DMSP synthesis
activity (nmol)

DMSP synthesis gene

Hot1 (bottom water)

LXJ035

Alteromonas macleodii

0.29

ROV279 (water 40 m from bottom)

LXJ021

Thalassospira profundimaris

1.84

mmtN^[34]

ROV277 (bottom water)

LXJ027

Thalassospira profundimaris

2.86

mmtN^[34]

ROV272 (5−6 cm)

LXJ008

Thalassospira profundimaris

0.30

mmtN^[34]

ROV277 (8−10 cm)

LXJ110

Idiomarina loihiensis

0.47

Shinkaia crosnieri (bristle)

LXJ113

Pseudoalteromonas shioyasakiensis

0.41

LXJ117

Pseudooceanicola marinus

3.18

dsyB^[29]

Strain source	Strain number	Species	DMSP demethylation activity	DMSP cleavage activity (nmol/h)
DMSP cleavage rate over 0.10 nmol/h. DMSP lysed strains that can produce MeSH are indicated by “+”, and those cannot produce MeSH are indicated by “−”.
CTD03 (bottom water)	LXJ198	Hyphomonas oceanitis	−	1.58
LXJ143	Pseudohoeflea suaedae	−	1.57
LXJ144	Pseudomonas stutzeri	−	1.27
LXJ145	Pseudohoeflea suaedae	−	1.62
LXJ197	Staphylococcus cohnii	−	0.12
LXJ199	Nesterenkonia halobia	−	0.17
C1 (105−108 cm)	LXJ231	Sulfitobacter pontiacus	−	1.83
LXJ232	Sulfitobacter pontiacus	−	1.83
ROV278 (bottom water)	LXJ189	Glutamicibacter creatinolyticus	−	1.35
LXJ190	Bacillus spizizenii	−	1.21
LXJ268	Alcanivorax dieselolei	−	1.89
LXJ269	Marinobacter nauticus	−	0.20
Shinkaia crosnieri (male gonad)	LXJ165	Marinobacter flavimaris	+	1.82
LXJ166	Marinobacter flavimaris	+	1.74
LXJ177	Glutamicibacter creatinolyticus	−	0.15
Mussel (visceral mass)	LXJ194	Hyphomonas oceanitis	−	1.67
LXJ155	Glutamicibacter creatinolyticus	−	0.22
LXJ193	Glutamicibacter creatinolyticus	−	0.13
ROV278 (6−8 cm)	LXJ258	Glutamicibacter creatinolyticus	−	0.39
LXJ260	Brachybacterium paraconglomeratum	−	0.92
LXJ195	Glutamicibacter creatinolyticus	−	0.18
ROV279 (6−8 cm)	LXJ261	Staphylococcus equorum subsp. linens	−	0.91
LXJ262	Staphylococcus cohnii	−	0.52
RYSHW (bottom sediments)	LXJ271	Shewanella xiamenensis	+	0.90
LXJ270	Georgenia muralis	−	0.12
LXJ273	Shewanella seohaensis	−	0.20
CTD03 (surface water)	LXJ186	Micrococcus endophyticus	−	0.12
CTD03 (800 m water)	LXJ200	Pseudohoeflea suaedae	−	0.15
LXJ245	Exiguobacterium mexicanum	−	0.11
Hot1 (5 m water)	LXJ205	Pseudohoeflea suaedae	−	0.16
Hot1 (1 000 m water)	LXJ148	Pseudohoeflea suaedae	−	0.30
LXJ149	Idiomarina loihiensis	−	0.14
QY01 (5−10 cm)	LXJ134	Glutamicibacter creatinolyticus	−	0.14
LXJ214	Micrococcus endophyticus	−	0.15
LXJ215	Micrococcus luteus	−	0.15
C2- (0−5 cm)	LXJ136	Glutamicibacter creatinolyticus	−	0.19
C2- (235−240 cm)	LXJ182	Glutamicibacter creatinolyticus	−	0.13
C1 (0−3 cm)	LXJ201	Paracoccus halotolerans	−	0.22
LXJ202	Glutamicibacter creatinolyticus	−	0.17
LXJ223	Kocuria palustris	−	0.18
LXJ224	Halomonas meridiana	−	0.19
C1 (54−57 cm)	LXJ137	Glutamicibacter creatinolyticus	−	0.18
ROV277 (0−2 cm)	LXJ241	Staphylococcus equorum subsp. linens	−	0.19
ROV278 (0−2 cm)	LXJ251	Marinobacter nauticus	−	0.13
LXJ253	Micrococcus luteus	−	0.28
ROV279 (water 5 m from bottom)	LXJ181	Micrococcus luteus	−	0.15
Shinkaia crosnieri (bristle)	LXJ170	Micrococcus endophyticus	−	0.12
Shinkaia crosnieri (egg)	LXJ159	Glutamicibacter creatinolyticus	−	0.21
LXJ162	Staphylococcus equorum subsp. linens	−	0.13
LXJ163	Kocuria rosea	−	0.12
LXJ176	Glutamicibacter arilaitensis	−	0.14
Mussel (gill)	LXJ152	Glutamicibacter creatinolyticus	−	0.12
Mussel (mantle)	LXJ158	Glutamicibacter creatinolyticus	−	0.24
Mussel (foot)	LXJ156	Glutamicibacter creatinolyticus	−	0.19
LXJ157	Glutamicibacter creatinolyticus	−	0.22

Strain source

Strain
number

Species

DMSP demethylation
activity

DMSP cleavage
activity (nmol/h)

DMSP cleavage rate over 0.10 nmol/h. DMSP lysed strains that can produce MeSH are indicated by “+”, and those cannot produce MeSH are indicated by “−”.

CTD03 (bottom water)

LXJ198

Hyphomonas oceanitis

−

1.58

LXJ143

Pseudohoeflea suaedae

−

1.57

LXJ144

Pseudomonas stutzeri

−

1.27

LXJ145

Pseudohoeflea suaedae

−

1.62

LXJ197

Staphylococcus cohnii

−

0.12

LXJ199

Nesterenkonia halobia

−

0.17

C1 (105−108 cm)

LXJ231

Sulfitobacter pontiacus

−

1.83

LXJ232

Sulfitobacter pontiacus

−

1.83

ROV278 (bottom water)

LXJ189

Glutamicibacter creatinolyticus

−

1.35

LXJ190

Bacillus spizizenii

−

1.21

LXJ268

Alcanivorax dieselolei

−

1.89

LXJ269

Marinobacter nauticus

−

0.20

Shinkaia crosnieri (male gonad)

LXJ165

Marinobacter flavimaris

1.82

LXJ166

Marinobacter flavimaris

1.74

LXJ177

Glutamicibacter creatinolyticus

−

0.15

Mussel (visceral mass)

LXJ194

Hyphomonas oceanitis

−

1.67

LXJ155

Glutamicibacter creatinolyticus

−

0.22

LXJ193

Glutamicibacter creatinolyticus

−

0.13

ROV278 (6−8 cm)

LXJ258

Glutamicibacter creatinolyticus

−

0.39

LXJ260

Brachybacterium paraconglomeratum

−

0.92

LXJ195

Glutamicibacter creatinolyticus

−

0.18

ROV279 (6−8 cm)

LXJ261

Staphylococcus equorum subsp. linens

−

0.91

LXJ262

Staphylococcus cohnii

−

0.52

RYSHW (bottom sediments)

LXJ271

Shewanella xiamenensis

0.90

LXJ270

Georgenia muralis

−

0.12

LXJ273

Shewanella seohaensis

−

0.20

CTD03 (surface water)

LXJ186

Micrococcus endophyticus

−

0.12

CTD03 (800 m water)

LXJ200

Pseudohoeflea suaedae

−

0.15

LXJ245

Exiguobacterium mexicanum

−

0.11

Hot1 (5 m water)

LXJ205

Pseudohoeflea suaedae

−

0.16

Hot1 (1 000 m water)

LXJ148

Pseudohoeflea suaedae

−

0.30

LXJ149

Idiomarina loihiensis

−

0.14

QY01 (5−10 cm)

LXJ134

Glutamicibacter creatinolyticus

−

0.14

LXJ214

Micrococcus endophyticus

−

0.15

LXJ215

Micrococcus luteus

−

0.15

C2- (0−5 cm)

LXJ136

Glutamicibacter creatinolyticus

−

0.19

C2- (235−240 cm)

LXJ182

Glutamicibacter creatinolyticus

−

0.13

C1 (0−3 cm)

LXJ201

Paracoccus halotolerans

−

0.22

LXJ202

Glutamicibacter creatinolyticus

−

0.17

LXJ223

Kocuria palustris

−

0.18

LXJ224

Halomonas meridiana

−

0.19

C1 (54−57 cm)

LXJ137

Glutamicibacter creatinolyticus

−

0.18

ROV277 (0−2 cm)

LXJ241

Staphylococcus equorum subsp. linens

−

0.19

ROV278 (0−2 cm)

LXJ251

Marinobacter nauticus

−

0.13

LXJ253

Micrococcus luteus

−

0.28

ROV279 (water 5 m from bottom)

LXJ181

Micrococcus luteus

−

0.15

Shinkaia crosnieri (bristle)

LXJ170

Micrococcus endophyticus

−

0.12

Shinkaia crosnieri (egg)

LXJ159

Glutamicibacter creatinolyticus

−

0.21

LXJ162

Staphylococcus equorum subsp. linens

−

0.13

LXJ163

Kocuria rosea

−

0.12

LXJ176

Glutamicibacter arilaitensis

−

0.14

Mussel (gill)

LXJ152

Glutamicibacter creatinolyticus

−

0.12

Mussel (mantle)

LXJ158

Glutamicibacter creatinolyticus

−

0.24

Mussel (foot)

LXJ156

Glutamicibacter creatinolyticus

−

0.19

LXJ157

Glutamicibacter creatinolyticus

−

0.22