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Yan C, Zhang K, Shi S, Jian L, Chen B, Quadri SR, Tian X. Alterisphingorhabdus coralli gen. nov. sp. nov., a novel aerobic anoxygenic phototrophic bacteria isolated from reef-building coral. Int J Syst Evol Microbiol 2024; 74. [PMID: 39570654 DOI: 10.1099/ijsem.0.006577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2024] Open
Abstract
The photosynthetic microorganisms within the coral holobiont produce energy and organic compounds through photosynthesis, which are vital for the biocalcification and heat tolerance of coral hosts. However, aerobic anoxygenic phototrophic bacteria (AAPB), which are one of the most important photosynthetic microorganisms, have not been thoroughly investigated in this environment. In this study, a novel AAPB, SCSIO 66989T, was isolated from the reef-building coral Favia sp. and considered a beneficial microorganism for corals (BMC). The polyphasic taxonomic analysis showed that it had the highest similarities with Parasphingorhabdus litoris DSM 22379T (95.9%) and Altererythrobacter ishigakiensis ATCC BAA-2084T (95.7%). Phylogenetic analysis showed that it formed an independent clade, distinguishing it from other genera within the family Sphingomonadaceae. The predominant fatty acids were C18 : 1 ω7c and/or C18 : 1 ω6c and C16 : 0. The major respiratory quinone was ubiquinone-10 (Q-10). Sphingolipid, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine were the diagnostic polar lipids. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between SCSIO 66989T and the type strains of P. litoris DSM 22379T and A. ishigakiensis ATCC BAA-2084T were 69.2-70.0%, 58.6-61.2% and 19.2-19.7%, respectively. These results indicate that strain SCSIO 66989T represents a new species of a novel genus in the family Sphingomonadaceae, for which the name Alterisphingorhabdus coralli gen. nov. sp. nov. is proposed.
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Affiliation(s)
- Chang Yan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Kun Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, PR China
| | - Songbiao Shi
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Lili Jian
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Beilin Chen
- School of Basic Medical Sciences, Guangdong Medical University, Dongguan 523808, PR China
| | - Syed Raziuddin Quadri
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Northern Border University, Arar-91431, Northern Borders, Kingdom of Saudi Arabia
| | - Xinpeng Tian
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
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Wang W, Wang Y, Jin K, Yang X, Sui Y, Zou B. Towards Efficient White-light Emission in Sulfur Dots through Surface Charge Engineering. Angew Chem Int Ed Engl 2024:e202415383. [PMID: 39322614 DOI: 10.1002/anie.202415383] [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: 08/12/2024] [Revised: 09/24/2024] [Accepted: 09/25/2024] [Indexed: 09/27/2024]
Abstract
Sulfur dots (SDs) have emerged as promising photoluminescence (PL) materials owing to their intrinsic merits such as abundant electronic effects, outstanding biocompatibility and available photocatalytic activity. Typically based on quantum confinement effects, SDs are reported usually confined emission in blue-to-green region. However, it is challenging to achieve their broad emission tunability in the visible region, restricted by inherent band gap of bulk sulfur (ca. 2.79 eV). Herein, we present white-light-emitting SDs achieved by surface charge engineering that hybridizes the surface of SDs with oleylamine. The resulting SDs exhibit broadband emissions (full width at half maximum of 187 nm) with PL quantum yields of up to 12.1 % and Commission International de I'Eclairage color coordinates of (0.27, 0.32). Detailed experimental and theoretical analysis reveal that the strong orbital coupling between oleylamine and sulfur on the hybrid surfaces of the SDs causes electron delocalization, leading to the generation of low-energy charge transfer (CT) states. These CT states are highly sensitive to sulfur-oleylamine hybrid structures, which complicate the transition dynamics and promote multi-energy emissions, accounting for efficient white-light emission. The demonstration of white-light SDs based on surface charge engineering is an important step towards the development of sulfur-based PL materials.
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Affiliation(s)
- Weibin Wang
- State Key Laboratory of Superhard Materials, Synergetic Extreme Condition High-Pressure Science Center, College of Physics, Jilin University, Changchun, 130012, P. R. China
| | - Yixuan Wang
- State Key Laboratory of Superhard Materials, Synergetic Extreme Condition High-Pressure Science Center, College of Physics, Jilin University, Changchun, 130012, P. R. China
| | - Kaixiang Jin
- State Key Laboratory of Superhard Materials, Synergetic Extreme Condition High-Pressure Science Center, College of Physics, Jilin University, Changchun, 130012, P. R. China
| | - Xinyi Yang
- State Key Laboratory of Superhard Materials, Synergetic Extreme Condition High-Pressure Science Center, College of Physics, Jilin University, Changchun, 130012, P. R. China
| | - Yongming Sui
- State Key Laboratory of Superhard Materials, Synergetic Extreme Condition High-Pressure Science Center, College of Physics, Jilin University, Changchun, 130012, P. R. China
| | - Bo Zou
- State Key Laboratory of Superhard Materials, Synergetic Extreme Condition High-Pressure Science Center, College of Physics, Jilin University, Changchun, 130012, P. R. China
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Ye X, Wang Z, Hu X, Xie P, Liu Y. Differential evaluation of sulfur oxides in the natural lake water samples by carbazole-furan fluorescent probe. CHEMOSPHERE 2024; 352:141308. [PMID: 38280644 DOI: 10.1016/j.chemosphere.2024.141308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 01/29/2024]
Abstract
Water bodies are frequently polluted, with sulfur oxides being the most common form of water pollution. Therefore, developing a detection mechanism for sulfur oxides in water bodies is particularly urgent. A new fluorescent probe YX-KZBD was designed and developed. This probe releases fluorescent signals with its own sulfurous acid recognition site, detects sulfurous acid based on the Michael addition reaction, and evaluates the pollution degree of sulfur oxides in the water environment through the transformation mode of the sulfur cycle. This probe has high energy transfer efficiency in aqueous solutions. In addition, the fluorescence data obtained by analyzing the water samples were linearly fitted with the gene abundance values of the functional genes of sulfur-producing bacteria, and a significant correlation was obtained. The Kriging interpolation model was used to evaluate the sulfate content distribution at each sampling point to understand the distribution of sulfur oxides in natural water intuitively. The fluorescence signal excited by the probe was also combined with a real-time quantitative polymerase chain reaction (qPCR), and sulfate-reducing and sulfur-oxidizing bacteria were introduced in the sulfur cycle, providing a new method to assess the extent of water pollution effectively.
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Affiliation(s)
- Xiao Ye
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, PR China; Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650500, PR China
| | - Zhaomin Wang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, PR China; Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650500, PR China
| | - Xiangyu Hu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, PR China; Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650500, PR China
| | - Ping Xie
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, PR China; Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
| | - Yong Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, PR China; Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650500, PR China.
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Römling U. Cyclic di-GMP signaling-Where did you come from and where will you go? Mol Microbiol 2023; 120:564-574. [PMID: 37427497 DOI: 10.1111/mmi.15119] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/17/2023] [Accepted: 06/22/2023] [Indexed: 07/11/2023]
Abstract
Microbes including bacteria are required to respond to their often continuously changing ecological niches in order to survive. While many signaling molecules are produced as seemingly circumstantial byproducts of common biochemical reactions, there are a few second messenger signaling systems such as the ubiquitous cyclic di-GMP second messenger system that arise through the synthesis of dedicated multidomain enzymes triggered by multiple diverse external and internal signals. Being one of the most numerous and widespread signaling system in bacteria, cyclic di-GMP signaling contributes to adjust physiological and metabolic responses in all available ecological niches. Those niches range from deep-sea and hydrothermal springs to the intracellular environment in human immune cells such as macrophages. This outmost adaptability is possible by the modularity of the cyclic di-GMP turnover proteins which enables coupling of enzymatic activity to the diversity of sensory domains and the flexibility in cyclic di-GMP binding sites. Nevertheless, commonly regulated fundamental microbial behavior include biofilm formation, motility, and acute and chronic virulence. The dedicated domains carrying out the enzymatic activity indicate an early evolutionary origin and diversification of "bona fide" second messengers such as cyclic di-GMP which is estimated to have been present in the last universal common ancestor of archaea and bacteria and maintained in the bacterial kingdom until today. This perspective article addresses aspects of our current view on the cyclic di-GMP signaling system and points to knowledge gaps that still await answers.
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Affiliation(s)
- Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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Lu W, Wang L, Liang J, Lu Y, Wang J, Fu YV. Dynamically Quantifying Intracellular Elemental Sulfur and Predicting Pertinent Gene Transcription by Raman Spectroscopy in Living Cells. Anal Chem 2023. [PMID: 37330921 DOI: 10.1021/acs.analchem.3c00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The ability to monitor changes in metabolites and corresponding gene transcription within living cells is highly desirable. However, most current assays for quantification of metabolites or for gene transcription are destructive, precluding tracking the real-time dynamics of living cells. Here, we used the intracellular elemental sulfur in a Thiophaeococcus mangrovi cell as a proof-of-concept to link the quantity of metabolites and relevant gene transcription in living cells by a nondestructive Raman approach. Raman spectroscopy was utilized to quantify intracellular elemental sulfur noninvasively, and a computational mRR (mRNA and Raman) model was developed to infer the transcription of genes relevant to elemental sulfur. The results showed a significant linear correlation between the exponentially transformed Raman spectral intensity of intracellular elemental sulfur and the mRNA levels of genes encoding sulfur globule proteins in T. mangrovi. The mRR model was verified independently in two genera of Thiocapsa and Thiorhodococcus, and the mRNA levels predicted by mRR showed high consistency with actual gene expression detected by real-time polymerase chain reaction (PCR). This approach could enable noninvasive assessment of the quantity of metabolites and link the pertinent gene expression profiles in living cells, providing useful baseline data to spectroscopically map various omics in real time.
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Affiliation(s)
- Weilai Lu
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing 100101, China
| | - Lu Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Liang
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Lu
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yu Vincent Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
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Römling U, Möglich A. Seeing the light brings more food in the deep sea. EMBO J 2023:e114091. [PMID: 37051729 DOI: 10.15252/embj.2023114091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/06/2023] [Indexed: 04/14/2023] Open
Abstract
Cyclic di-GMP signaling regulates sessile-to-motile lifestyle transition and associated physiological and metabolic features in bacteria. The presence of potential cyclic di-GMP turnover proteins in deepest branching bacteria indicates that cyclic di-GMP is an ancient signaling molecule. In this issue of The EMBO Journal, Cai et al (2023) describe light-induced activation of a thiosulfate oxidation pathway in the deep-sea cold-seep bacterium Qipengyuania flava, thus coupling cyclic di-GMP with the regulation of the global abiotic sulfur cycle.
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Affiliation(s)
- Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andreas Möglich
- Department of Biochemistry, Universität Bayreuth, Bayreuth, Germany
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