1
|
Zhou DD, Xu XD, Zhang BZ, Feng JX, Zhang J. Tropicibacter oceani sp. nov., a novel sulfur-metabolizing bacteria isolated from the intertidal zone sediment of Chinese Yellow Sea. Antonie Van Leeuwenhoek 2023; 116:1337-1344. [PMID: 37833447 DOI: 10.1007/s10482-023-01890-5] [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: 07/31/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023]
Abstract
In this study, we reported a Gram-stain-negative, rod-shaped, atrichous, and aerobic bacterial strain named YMD87T, which was isolated from the intertidal zone sediment of Chinese Yellow Sea. Growth of strain YMD87T occurred at 10.0-40.0 °C (optimum, 25-30 °C), pH 4.0-12.0 (optimum, 8.0) and with 0-6.0% (w/v) NaCl (optimum, 0.0-2.0%). Phylogenetic tree analysis based on 16S rRNA gene sequence indicated that strain YMD87T belonged to the genus Tropicibacter and was closely related to Tropicibacter alexandrii LMIT003T (97.2% sequence similarity). Genomic analysis indicated that strain YMD87T contains a circular chromosome of 3,932,460 bp with G + C content of 63.8% and three circular plasmids of 116,492 bp, 49,209 bp and 49,673 bp, with G + C content of 64.3%. Genomic functional analysis revealed that strain YMD87T is potential a novel sulfur-metabolizing bacteria. The predominant respiratory quinone of YMD87T was ubiquinone-10 (Q-10). The major polar lipids of YMD87T contained phosphatidylglycerol, phosphatidylethanolamine, five unidentified lipids, five unidentified phospholipids, phosphatidylcholine, unidentified glycolipid and five unidentified aminolipids. The major fatty acids of strain YMD87T contained C12:1 3-OH, C16:0, and summed feature 8 (C18:1 ω7c or/and C18:1 ω6c). Phylogenetic, physiological, biochemical and morphological analyses suggested that strain YMD87T represents a novel species of the genus Tropicibacter, and the name Tropicibacter oceani sp. nov is proposed. The type strain is YMD87T (= MCCC 1K08473T = KCTC 92856 T).
Collapse
Affiliation(s)
- Dan-Dan Zhou
- School of Ocean, Yantai University, 30 QingQuan Road, Yantai, 264005, China
| | - Xiu-Dan Xu
- School of Ocean, Yantai University, 30 QingQuan Road, Yantai, 264005, China
| | - Bin-Zhe Zhang
- School of Ocean, Yantai University, 30 QingQuan Road, Yantai, 264005, China
| | - Ji-Xing Feng
- School of Ocean, Yantai University, 30 QingQuan Road, Yantai, 264005, China
| | - Jian Zhang
- School of Ocean, Yantai University, 30 QingQuan Road, Yantai, 264005, China.
| |
Collapse
|
2
|
Réveillon D, Savar V, Schaefer E, Chevé J, Halm-Lemeille MP, Hervio-Heath D, Travers MA, Abadie E, Rolland JL, Hess P. Tetrodotoxins in French Bivalve Mollusks-Analytical Methodology, Environmental Dynamics and Screening of Bacterial Strain Collections. Toxins (Basel) 2021; 13:740. [PMID: 34822524 PMCID: PMC8618394 DOI: 10.3390/toxins13110740] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/28/2022] Open
Abstract
Tetrodotoxins (TTXs) are potentially lethal paralytic toxins that have been identified in European shellfish over recent years. Risk assessment has suggested comparatively low levels (44 µg TTX-equivalent/kg) but stresses the lack of data on occurrence. Both bacteria and dinoflagellates were suggested as possible biogenic sources, either from an endogenous or exogenous origin. We thus investigated TTXs in (i) 98 shellfish samples and (ii) 122 bacterial strains, isolated from French environments. We optimized a method based on mass spectrometry, using a single extraction step followed by ultrafiltration without Solid Phase Extraction and matrix-matched calibration for both shellfish and bacterial matrix. Limits of detection and quantification were 6.3 and 12.5 µg/kg for shellfish and 5.0 and 10 µg/kg for bacterial matrix, respectively. Even though bacterial matrix resulted in signal enhancement, no TTX analog was detected in any strain. Bivalves (either Crassostrea gigas or Ruditapes philippinarum) were surveyed in six French production areas over 2.5-3 month periods (2018-2019). Concentrations of TTX ranged from 'not detected' to a maximum of 32 µg/kg (Bay of Brest, 17 June 2019), with events lasting 2 weeks at maximum. While these results are in line with previous studies, they provide new data of TTX occurrence and confirm that the link between bacteria, bivalves and TTX is complex.
Collapse
Affiliation(s)
- Damien Réveillon
- Ifremer, DYNECO, Laboratoire Phycotoxines, F-44000 Nantes, France; (V.S.); (E.S.)
| | - Véronique Savar
- Ifremer, DYNECO, Laboratoire Phycotoxines, F-44000 Nantes, France; (V.S.); (E.S.)
| | - Estelle Schaefer
- Ifremer, DYNECO, Laboratoire Phycotoxines, F-44000 Nantes, France; (V.S.); (E.S.)
| | | | | | - Dominique Hervio-Heath
- LEMAR, Université de Brest, Ifremer, CNRS, IRD, F-29280 Plouzané, France;
- Ifremer, SG2M, Laboratoire LSEM, F-29280 Plouzané, France
| | - Marie-Agnès Travers
- Ifremer, SG2M, Laboratoire LGPMM, F-17390 La Tremblade, France;
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, F-34000 Montpellier, France;
| | - Eric Abadie
- Ifremer, Biodivenv, F-97231 Le Robert, France;
- MARBEC, Université de Montpellier, IRD, Ifremer, CNRS, F-34000 Montpellier, France
| | - Jean-Luc Rolland
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, F-34000 Montpellier, France;
- MARBEC, Université de Montpellier, IRD, Ifremer, CNRS, F-34000 Montpellier, France
| | - Philipp Hess
- Ifremer, DYNECO, Laboratoire Phycotoxines, F-44000 Nantes, France; (V.S.); (E.S.)
| |
Collapse
|
3
|
Isaac A, Francis B, Amann RI, Amin SA. Tight Adherence (Tad) Pilus Genes Indicate Putative Niche Differentiation in Phytoplankton Bloom Associated Rhodobacterales. Front Microbiol 2021; 12:718297. [PMID: 34447362 PMCID: PMC8383342 DOI: 10.3389/fmicb.2021.718297] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/19/2021] [Indexed: 11/14/2022] Open
Abstract
The multiple interactions of phytoplankton and bacterioplankton are central for our understanding of aquatic environments. A prominent example of those is the consistent association of diatoms with Alphaproteobacteria of the order Rhodobacterales. These photoheterotrophic bacteria have traditionally been described as generalists that scavenge dissolved organic matter. Many observations suggest that members of this clade are specialized in colonizing the microenvironment of diatom cells, known as the phycosphere. However, the molecular mechanisms that differentiate Rhodobacterales generalists and phycosphere colonizers are poorly understood. We investigated Rhodobacterales in the North Sea during the 2010–2012 spring blooms using a time series of 38 deeply sequenced metagenomes and 10 metaproteomes collected throughout these events. Rhodobacterales metagenome assembled genomes (MAGs) were recurrently abundant. They exhibited the highest gene enrichment and protein expression of small-molecule transporters, such as monosaccharides, thiamine and polyamine transporters, and anaplerotic pathways, such as ethylmalonyl and propanoyl-CoA metabolic pathways, all suggestive of a generalist lifestyle. Metaproteomes indicated that the species represented by these MAGs were the dominant suppliers of vitamin B12 during the blooms, concomitant with a significant enrichment of genes related to vitamin B12 biosynthesis suggestive of association with diatom phycospheres. A closer examination of putative generalists and colonizers showed that putative generalists had persistently higher relative abundance throughout the blooms and thus produced more than 80% of Rhodobacterales transport proteins, suggesting rapid growth. In contrast, putative phycosphere colonizers exhibited large fluctuation in relative abundance across the different blooms and correlated strongly with particular diatom species that were dominant during the blooms each year. The defining feature of putative phycosphere colonizers is the presence of the tight adherence (tad) gene cluster, which is responsible for the assembly of adhesive pili that presumably enable attachment to diatom hosts. In addition, putative phycosphere colonizers possessed higher prevalence of secondary metabolite biosynthetic gene clusters, particularly homoserine lactones, which can regulate bacterial attachment through quorum sensing. Altogether, these findings suggest that while many members of Rhodobacterales are competitive during diatom blooms, only a subset form close associations with diatoms by colonizing their phycospheres.
Collapse
Affiliation(s)
- Ashley Isaac
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ben Francis
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Shady A Amin
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| |
Collapse
|
4
|
Li N, He XY, Liu NH, Gu TJ, Li J, Geng YH, Zhang S, Wang P, Fu HH, Shi M, Chen XL, Zhang YZ, Zhang XY, Qin QL. Tritonibacter aquimaris sp. nov. and Tritonibacter litoralis sp. nov., two novel members of the Roseobacter group isolated from coastal seawater. Antonie Van Leeuwenhoek 2021; 114:787-798. [PMID: 33782795 DOI: 10.1007/s10482-021-01558-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/08/2021] [Indexed: 11/26/2022]
Abstract
Two Gram-stain-negative bacterial strains, SM1969T and SM1979T, were isolated from coastal surface seawater of Qingdao, China. They were taxonomically characterized by the phylogenetic, genomic, chemotaxonomic and phenotypic analyses. The two strains shared 97.0% 16S rRNA gene sequence similarity with each other and the highest similarity (96.8-97.5%) with type strains of six species in the genera Shimia, Tritonibacter and Tropicibacter in the Roseobacter group of the family Rhodobacteraceae. In the phylogenetic tree based on single-copy orthologous clusters (OCs), both strains clustered with known species of the genus Tritonibacter and together formed a separate branch adjacent to Tritonibacter ulvae. Although sharing many chemotaxonomic and phenotypic characteristics, the two strains could be differentiated from each other and closely related species by numerous traits. Particularly, strain SM1969T was found to have a DMSP lyase coding gene dddW in its genome and have the ability to produce DMS from DMSP while strain SM1979T was not. The average nucleotide identity and in silico DNA-DNA hybridization values between strains SM1969T and SM1979T and type strains of closely related species were all below the thresholds to discriminate bacterial species, demonstrating that they constitute two new species in the genus Tritonibacter. The names Tritonibacter aquimaris sp. nov. and Tritonibacter litoralis sp. nov. are proposed for the two new species, with type strains being SM1969T (= MCCC 1K04320T = KCTC 72843T) and SM1979T (= MCCC 1K04321T = KCTC 72842T), respectively.
Collapse
Affiliation(s)
- Na Li
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Xiao-Yan He
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Ning-Hua Liu
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Tie-Ji Gu
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Jian Li
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Yu-Hui Geng
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Shan Zhang
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Peng Wang
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China
| | - Hui-Hui Fu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China
| | - Mei Shi
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China.
| |
Collapse
|