1
|
Zhang M, Tong X, Wang W, Wang J, Qu W. Agarose biodegradation by deep-sea bacterium Vibrio natriegens WPAGA4 with the agarases through horizontal gene transfer. J Basic Microbiol 2024; 64:e2300521. [PMID: 37988660 DOI: 10.1002/jobm.202300521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/10/2023] [Accepted: 11/01/2023] [Indexed: 11/23/2023]
Abstract
This study aimed to reveal the importance of horizontal gene transfer (HGT) for the agarose-degrading ability and the related degradation pathway of a deep-sea bacterium Vibrio natriegens WPAGA4, which was rarely reported in former works. A total of four agarases belonged to the GH50 family, including Aga3418, Aga3419, Aga3420, and Aga3472, were annotated and expressed in Escherichia coli cells. The agarose degradation products of Aga3418, Aga3420, and Aga3472 were neoagarobiose, while those of Aga3419 were neoagarobiose and neoagarotetraose. The RT-qPCR analysis showed that the expression level ratio of Aga3418, Aga3419, Aga3420, and Aga3472 was stable at about 1:1:1.5:2.5 during the degradation, which indicated the optimal expression level ratio of the agarases for agarose degradation by V. natriegens WPAGA4. Based on the genomic information, three of four agarases and other agarose-degrading related genes were in a genome island with a G + C content that was obviously lower than that of the whole genome of V. natriegens WPAGA4, indicating that these agarose-degrading genes were required through HGT. Our results demonstrated that the expression level ratio instead of the expression level itself of agarase genes was crucial for agarose degradation by V. natriegens WPAGA4, and HGT occurred in the deep-sea environment, thereby promoting the deep-sea carbon cycle and providing a reference for studying the evolution and transfer pathways of agar-related genes.
Collapse
Affiliation(s)
- Mengyuan Zhang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
- Zhejiang Ocean University-University of Pisa Marine Graduate School, Zhoushan, China
| | - Xiufang Tong
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Wenxin Wang
- Zhejiang Ocean University-University of Pisa Marine Graduate School, Zhoushan, China
| | - Jianxin Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Wu Qu
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| |
Collapse
|
2
|
Liu M, Yin F, Zhao W, Tian P, Zhou Y, Jia Z, Huang K, Ding Y, Xiao J, Niu W, Wang X. Diversity of Culturable Bacteria from the Coral Reef Areas in the South China Sea and Their Agar-Degrading Abilities. Microorganisms 2024; 12:187. [PMID: 38258013 PMCID: PMC10818321 DOI: 10.3390/microorganisms12010187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
The South China Sea (SCS) is abundant in marine microbial resources with high primary productivity, which is crucial for sustaining the coral reef ecosystem and the carbon cycle. Currently, research on the diversity of culturable bacteria in the SCS is relatively extensive, yet the culturable bacteria in coral reefs has been poorly understood. In this study, we analyzed the bacterial community structure of seawater samples among Daya Bay (Fujian Province), Qionghai (Hainan Province), Xisha Islands, and the southern South China Sea based on culturable methods and detected their abilities for agar degradation. There were 441 bacterial strains, belonging to three phyla, five classes, 43 genera, and 101 species, which were isolated by marine agar 2216E (MA; Becton Dickinson). Strains within Gammaproteobacteria were the dominant group, accounting for 89.6% of the total bacterial isolates. To investigate vibrios, which usually correlated with coral health, 348 isolates were obtained from TCBS agar, and all isolates were identified into three phylum, three classes, 14 orders, 25 families, and 48 genera. Strains belonging to the genus Vibrio had the greatest number (294 strains), indicating the high selectivity of TCBS agar for vibrios. Furthermore, nineteen strains were identified as potentially novel species according to the low 16S rRNA gene similarity (<98.65%), and 28 strains (15 species) had agar-degrading ability. These results indicate a high diversity of culturable bacteria in the SCS and a huge possibility to find novel and agar-degrading species. Our study provides valuable microbial resources to maintain the stability of coral ecosystems and investigate their roles in the marine carbon cycle.
Collapse
Affiliation(s)
- Mei Liu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (M.L.); (F.Y.); (W.Z.); (Y.Z.); (K.H.); (Y.D.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266071, China
| | - Fu Yin
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (M.L.); (F.Y.); (W.Z.); (Y.Z.); (K.H.); (Y.D.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266071, China
| | - Wenbin Zhao
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (M.L.); (F.Y.); (W.Z.); (Y.Z.); (K.H.); (Y.D.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266071, China
| | - Peng Tian
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, China; (P.T.); (Z.J.); (J.X.)
- Nansha Islands Coral Reef Ecosystem National Observation and Research Station, Guangzhou 510300, China
| | - Yi Zhou
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (M.L.); (F.Y.); (W.Z.); (Y.Z.); (K.H.); (Y.D.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266071, China
| | - Zhiyu Jia
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, China; (P.T.); (Z.J.); (J.X.)
- Nansha Islands Coral Reef Ecosystem National Observation and Research Station, Guangzhou 510300, China
| | - Keyi Huang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (M.L.); (F.Y.); (W.Z.); (Y.Z.); (K.H.); (Y.D.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266071, China
| | - Yunqi Ding
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (M.L.); (F.Y.); (W.Z.); (Y.Z.); (K.H.); (Y.D.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266071, China
| | - Jiaguang Xiao
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, China; (P.T.); (Z.J.); (J.X.)
- Nansha Islands Coral Reef Ecosystem National Observation and Research Station, Guangzhou 510300, China
| | - Wentao Niu
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, China; (P.T.); (Z.J.); (J.X.)
- Nansha Islands Coral Reef Ecosystem National Observation and Research Station, Guangzhou 510300, China
| | - Xiaolei Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (M.L.); (F.Y.); (W.Z.); (Y.Z.); (K.H.); (Y.D.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266071, China
| |
Collapse
|
3
|
Phillips EK, Shaffer JMC, Henson MW, Coelho JT, Martin MO, Thrash JC. Genome sequences of four agarolytic bacteria from the Bacteroidia and Gammaproteobacteria. Microbiol Resour Announc 2023; 12:e0066723. [PMID: 37812006 PMCID: PMC10652895 DOI: 10.1128/mra.00667-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 07/31/2023] [Indexed: 10/10/2023] Open
Abstract
Here we present the genomes of four marine agarolytic bacteria belonging to the Bacteroidota and Proteobacteria. Two genomes are closed and two are in draft form, but all are at least 99% complete and offer new opportunities to study agar-degradation in marine bacteria.
Collapse
Affiliation(s)
- Elise K. Phillips
- Department of Biology, University of Puget Sound, Tacoma, Washington, USA
| | | | - Michael W. Henson
- Department of Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Jordan T. Coelho
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Mark O. Martin
- Department of Biology, University of Puget Sound, Tacoma, Washington, USA
| | - J. Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| |
Collapse
|