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  • 1
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    Online Resource
    Distribution of bacterial genes driving dimethyl sulfide cycling in the polar oceans
    Springer Science and Business Media LLC ; 2021
    In:  Microbiome Vol. 9, No. 1 ( 2021-10-16)
    Details
    In: Microbiome, Springer Science and Business Media LLC, Vol. 9, No. 1 ( 2021-10-16)
    Abstract: Dimethyl sulfide (DMS) is the dominant volatile organic sulfur in global oceans. The predominant source of oceanic DMS is the cleavage of dimethylsulfoniopropionate (DMSP), which can be produced by marine bacteria and phytoplankton. Polar oceans, which represent about one fifth of Earth’s surface, contribute significantly to the global oceanic DMS sea-air flux. However, a global overview of DMS and DMSP cycling in polar oceans is still lacking and the key genes and the microbial assemblages involved in DMSP/DMS transformation remain to be fully unveiled. Results Here, we systematically investigated the biogeographic traits of 16 key microbial enzymes involved in DMS/DMSP cycling in 60 metagenomic samples from polar waters, together with 174 metagenome and 151 metatranscriptomes from non-polar Tara Ocean dataset. Our analyses suggest that intense DMS/DMSP cycling occurs in the polar oceans. DMSP demethylase (DmdA), DMSP lyases (DddD, DddP, and DddK), and trimethylamine monooxygenase (Tmm, which oxidizes DMS to dimethylsulfoxide) were the most prevalent bacterial genes involved in global DMS/DMSP cycling. Alphaproteobacteria (Pelagibacterales) and Gammaproteobacteria appear to play prominent roles in DMS/DMSP cycling in polar oceans. The phenomenon that multiple DMS/DMSP cycling genes co-occurred in the same bacterial genome was also observed in metagenome assembled genomes (MAGs) from polar oceans. The microbial assemblages from the polar oceans were significantly correlated with water depth rather than geographic distance, suggesting the differences of habitats between surface and deep waters rather than dispersal limitation are the key factors shaping microbial assemblages involved in DMS/DMSP cycling in polar oceans. Conclusions Overall, this study provides a global overview of the biogeographic traits of known bacterial genes involved in DMS/DMSP cycling from the Arctic and Antarctic oceans, laying a solid foundation for further studies of DMS/DMSP cycling in polar ocean microbiome at the enzymatic, metabolic, and processual levels.
    Type of Medium: Online Resource
    ISSN: 2049-2618
    URL: Article
    URL: Article
    DOI: 10.1186/s40168-021-01153-3
    DOI: 10.21203/rs.3.rs-1405853/v1
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2697425-3
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  • 2
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    d -Alanine Metabolism via d- Ala Aminotransferase by a Marine Gammaproteobacterium, Pseudoalteromonas sp. Strain CF6-2
    American Society for Microbiology ; 2022
    In:  Applied and Environmental Microbiology Vol. 88, No. 3 ( 2022-02-08)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 88, No. 3 ( 2022-02-08)
    Abstract: As the most abundant d- amino acid (DAA) in the ocean, d- alanine ( d -Ala) is a key component of peptidoglycan in the bacterial cell wall. However, the underlying mechanisms of bacterial metabolization of d- Ala through the microbial food web remain largely unknown. In this study, the metabolism of d- Ala by marine bacterium Pseudoalteromonas sp. strain CF6-2 was investigated. Based on genomic, transcriptional, and biochemical analyses combined with gene knockout, d- Ala aminotransferase was found to be indispensable for the catabolism of d- Ala in strain CF6-2. Investigation on other marine bacteria also showed that d- Ala aminotransferase gene is a reliable indicator for their ability to utilize d- Ala. Bioinformatic investigation revealed that d- Ala aminotransferase sequences are prevalent in genomes of marine bacteria and metagenomes, especially in seawater samples, and Gammaproteobacteria represents the predominant group containing d- Ala aminotransferase. Thus, Gammaproteobacteria is likely the dominant group to utilize d- Ala via d- Ala aminotransferase to drive the recycling and mineralization of d- Ala in the ocean. IMPORTANCE As the most abundant d- amino acid in the ocean, d- Ala is a component of the marine DON (dissolved organic nitrogen) pool. However, the underlying mechanism of bacterial metabolization of d- Ala to drive the recycling and mineralization of d- Ala in the ocean is still largely unknown. The results in this study showed that d- Ala aminotransferase is specific and indispensable for d- Ala catabolism in marine bacteria and that marine bacteria containing d- Ala aminotransferase genes are predominantly Gammaproteobacteria widely distributed in global oceans. This study reveals marine d- Ala-utilizing bacteria and the mechanism of their metabolization of d- Ala. The results shed light on the mechanisms of recycling and mineralization of d- Ala driven by bacteria in the ocean, which are helpful in understanding oceanic microbial-mediated nitrogen cycle.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/aem.02219-21
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2022
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 3
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    Correction to: Biogeographic traits of dimethyl sulfide and dimethylsulfoniopropionate cycling in polar oceans
    Springer Science and Business Media LLC ; 2021
    In:  Microbiome Vol. 9, No. 1 ( 2021-12)
    Details
    In: Microbiome, Springer Science and Business Media LLC, Vol. 9, No. 1 ( 2021-12)
    Type of Medium: Online Resource
    ISSN: 2049-2618
    URL: Article
    DOI: 10.1186/s40168-021-01182-y
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2697425-3
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  • 4
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    Image_1.TIF
    Frontiers Media SA ; 2021
    In:  Frontiers in Microbiology Vol. 12 ( 2021-9-24)
    Details
    In: Frontiers in Microbiology, Frontiers Media SA, Vol. 12 ( 2021-9-24)
    Abstract: Dimethylsulfide (DMS) and dimethylsulfoxide (DMSO) are widespread in marine environment, and are important participants in the global sulfur cycle. Microbiol oxidation of DMS to DMSO represents a major sink of DMS in marine surface waters. The SAR11 clade and the marine Roseobacter clade (MRC) are the most abundant heterotrophic bacteria in the ocean surface seawater. It has been reported that trimethylamine monooxygenase (Tmm, EC 1.14.13.148) from both MRC and SAR11 bacteria likely oxidizes DMS to generate DMSO. However, the structural basis of DMS oxidation has not been explained. Here, we characterized a Tmm homolog from the SAR11 bacterium Pelagibacter sp. HTCC7211 (Tmm 7211 ). Tmm 7211 exhibits DMS oxidation activity in vitro . We further solved the crystal structures of Tmm 7211 and Tmm 7211 soaked with DMS, and proposed the catalytic mechanism of Tmm 7211 , which comprises a reductive half-reaction and an oxidative half-reaction. FAD and NADPH molecules are essential for the catalysis of Tmm 7211 . In the reductive half-reaction, FAD is reduced by NADPH. In the oxidative half-reaction, the reduced FAD reacts with O 2 to form the C4a-(hydro)peroxyflavin. The binding of DMS may repel the nicotinamide ring of NADP + , and make NADP + generate a conformational change, shutting off the substrate entrance and exposing the active C4a-(hydro)peroxyflavin to DMS to complete the oxidation of DMS. The proposed catalytic mechanism of Tmm 7211 may be widely adopted by MRC and SAR11 bacteria. This study provides important insight into the conversion of DMS into DMSO in marine bacteria, leading to a better understanding of the global sulfur cycle.
    Type of Medium: Online Resource
    ISSN: 1664-302X
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fmicb.2021.735793
    DOI: 10.3389/fmicb.2021.735793.s001
    DOI: 10.3389/fmicb.2021.735793.s002
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2587354-4
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  • 5
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    Ubiquitous occurrence of a dimethylsulfoniopropionate ABC transporter in abundant marine bacteria
    Springer Science and Business Media LLC ; 2023
    In:  The ISME Journal Vol. 17, No. 4 ( 2023-04), p. 579-587
    Details
    In: The ISME Journal, Springer Science and Business Media LLC, Vol. 17, No. 4 ( 2023-04), p. 579-587
    Abstract: Dimethylsulfoniopropionate (DMSP) is a ubiquitous organosulfur compound in marine environments with important functions in both microorganisms and global biogeochemical carbon and sulfur cycling. The SAR11 clade and marine Roseobacter group (MRG) represent two major groups of heterotrophic bacteria in Earth’s surface oceans, which can accumulate DMSP to high millimolar intracellular concentrations. However, few studies have investigated how SAR11 and MRG bacteria import DMSP. Here, through comparative genomics analyses, genetic manipulations, and biochemical analyses, we identified an ABC (ATP-binding cassette)-type DMSP-specific transporter, DmpXWV, in Ruegeria pomeroyi DSS-3, a model strain of the MRG. Mutagenesis suggested that DmpXWV is a key transporter responsible for DMSP uptake in strain DSS-3. DmpX, the substrate binding protein of DmpXWV, had high specificity and binding affinity towards DMSP. Furthermore, the DmpX DMSP-binding mechanism was elucidated from structural analysis. DmpX proteins are prevalent in the numerous cosmopolitan marine bacteria outside the SAR11 clade and the MRG, and dmpX transcription was consistently high across Earth’s entire global ocean. Therefore, DmpXWV likely enables pelagic marine bacteria to efficiently import DMSP from seawater. This study offers a new understanding of DMSP transport into marine bacteria and provides novel insights into the environmental adaption of marine bacteria.
    Type of Medium: Online Resource
    ISSN: 1751-7362 , 1751-7370
    URL: Article
    DOI: 10.1038/s41396-023-01375-3
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2299378-2
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  • 6
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    Mechanistic Insights into Substrate Recognition and Catalysis of a New Ulvan Lyase of Polysaccharide Lyase Family 24
    American Society for Microbiology ; 2021
    In:  Applied and Environmental Microbiology Vol. 87, No. 12 ( 2021-05-26)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 87, No. 12 ( 2021-05-26)
    Abstract: Ulvan is an important marine polysaccharide. Bacterial ulvan lyases play important roles in ulvan degradation and marine carbon cycling. Until now, only a small number of ulvan lyases have been characterized. Here, a new ulvan lyase, Uly1, belonging to polysaccharide lyase family 24 (PL24) from the marine bacterium Catenovulum maritimum , is characterized. The optimal temperature and pH for Uly1 to degrade ulvan are 40°C and pH 9.0, respectively. Uly1 degrades ulvan polysaccharides in the endolytic manner, mainly producing ΔRha3S, consisting of an unsaturated 4-deoxy- l - threo -hex-4-enopyranosiduronic acid and a 3-O-sulfated α- l -rhamnose. The structure of Uly1 was resolved at a 2.10-Å resolution. Uly1 adopts a seven-bladed β-propeller architecture. Structural and site-directed mutagenesis analyses indicate that four highly conserved residues, H128, H149, Y223, and R239, are essential for catalysis. H128 functions as both the catalytic acid and base, H149 and R239 function as the neutralizers, and Y223 plays a supporting role in catalysis. Structural comparison and sequence alignment suggest that Uly1 and many other PL24 enzymes may directly bind the substrate near the catalytic residues for catalysis, different from the PL24 ulvan lyase LOR_107, which adopts a two-stage substrate binding process. This study provides new insights into ulvan lyases and ulvan degradation. IMPORTANCE Ulvan is a major cell wall component of green algae of the genus Ulva. Many marine heterotrophic bacteria can produce extracellular ulvan lyases to degrade ulvan for a carbon nutrient. In addition, ulvan has a range of physiological bioactivities based on its specific chemical structure. Ulvan lyase thus plays an important role in marine carbon cycling and has great potential in biotechnological applications. However, only a small number of ulvan lyases have been characterized over the past 10 years. Here, based on biochemical and structural analyses, a new ulvan lyase of polysaccharide lyase family 24 is characterized, and its substrate recognition and catalytic mechanisms are revealed. Moreover, a new substrate binding process adopted by PL24 ulvan lyases is proposed. This study offers a better understanding of bacterial ulvan lyases and is helpful for studying the application potentials of ulvan lyases.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.00412-21
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2021
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
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  • 7
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    Lack of N-Terminal Segment of the Flagellin Protein Results in the Production of a Shortened Polar Flagellum in the Deep-Sea Sedimentary Bacterium Pseudoalteromonas sp. Strain SM9913
    American Society for Microbiology ; 2021
    In:  Applied and Environmental Microbiology Vol. 87, No. 21 ( 2021-10-14)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 87, No. 21 ( 2021-10-14)
    Abstract: Bacterial polar flagella, comprised of flagellin, are essential for bacterial motility. Pseudoalteromonas sp. strain SM9913 is a bacterium isolated from deep-sea sediments. Unlike other Pseudoalteromonas strains that have a long polar flagellum, strain SM9913 has an abnormally short polar flagellum. Here, we investigated the underlying reason for the short flagellum and found that a single-base mutation was responsible for the altered flagellar assembly. This mutation leads to the fragmentation of the flagellin gene into two genes, PSM_A2281 , encoding the core segment and the C-terminal segment, and PSM_A2282 , encoding the N-terminal segment, and only gene PSM_A2281 is involved in the production of the short polar flagellum. When a chimeric gene of PSM_A2281 and PSM_A2282 encoding an intact flagellin, A2281::82, was expressed, a long polar flagellum was produced, indicating that the N-terminal segment of flagellin contributes to the production of a polar flagellum of a normal length. Analyses of the simulated structures of A2281 and A2281::82 and that of the flagellar filament assembled with A2281::82 indicate that due to the lack of two α-helices, the core of the flagellar filament assembled with A2281 is incomplete and is likely too weak to support the stability and movement of a long flagellum. This mutation in strain SM9913 had little effect on its growth and only a small effect on its swimming motility, implying that strain SM9913 can live well with this mutation in natural sedimentary environments. This study provides a better understanding of the assembly and production of bacterial flagella. IMPORTANCE Polar flagella, which are essential organelles for bacterial motility, are comprised of multiple flagellin subunits. A flagellin molecule contains an N-terminal segment, a core segment, and a C-terminal segment. The results of this investigation of the deep-sea sedimentary bacterium Pseudoalteromonas sp. strain SM9913 demonstrate that a single-base mutation in the flagellin gene leads to the production of an incomplete flagellin without the N-terminal segment and that the loss of the N-terminal segment of the flagellin protein results in the production of a shortened polar flagellar filament. Our results shed light on the important function of the N-terminal segment of flagellin in the assembly and stability of bacterial flagellar filament.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.01527-21
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2021
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
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  • 8
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    Arsukibacterium indicum sp. nov., isolated from deep-sea sediment, and transfer of Rheinheimera tuosuensis and Rheinheimera perlucida to the genus Arsukibacterium as Arsukibacterium tuosuense comb. nov. and Arsukibacterium perlucidum comb. nov.
    Microbiology Society ; 2022
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 72, No. 7 ( 2022-07-19)
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 72, No. 7 ( 2022-07-19)
    Abstract: A Gram-stain-negative, aerobic, flagellated and rod-shaped bacterium, designated strain SM2107 T , was isolated from a deep-sea sediment sample collected from the Southwest Indian Ocean. Strain SM2107 T grew at 4–40 °C and with 0–10.0 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed casein, gelatin, chitin and DNA. The phylogenetic trees based on the 16S rRNA genes and single-copy orthologous clusters showed that strain SM2107 T , together with Rheinheimera tuosuensis , Rheinheimera perlucida and Arsukibacterium ikkense , formed a separate clade, having the highest similarity to the type strain of Rheinheimera tuosuensis (98.3%). The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol and the major cellular fatty acids were summed feature 8 (C 18 : 1  ω 7 c and/or C 18 : 1  ω 6 c ), C 16 : 0 , C 17 : 1 ω 8 с and summed feature 3 (C 16 : 1  ω 7 c and/or C 16 : 1  ω 6 c ). The only respiratory quinone was Q-8. The genomic DNA G+C content of strain SM2107 T was 48.8 %. The digital DNA–DNA hybridization values between strain SM2107 T and type strains of Rheinheimera tuosuensis , Rheinheimera perlucida and Arsukibacterium ikkense were 41.16, 37.70 and 31.80 %, while the average amino acid identity values between them were 87.59, 86.76 and 83.64 %, respectively. Based on the polyphasic evidence presented in this study, strain SM2107 T was considered to represent a novel species within the genus Arsukibacterium , for which the name Arsukibacterium indicum was proposed. The type strain is SM2107 T (=MCCC M24986 T =KCTC 82921 T ). Moreover, the transfer of Rheinheimera tuosuensis and Rheinheimera perlucida to the genus Arsukibacterium as Arsukibacterium tuosuense comb. nov. (type strain TS-T4 T =CGMCC 1.12461 T =JCM 19264 T ) and Arsukibacterium perlucidum comb. nov. (type strain BA131 T =LMG 23581 T =CIP 109200 T ) is also proposed.
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.005455
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2022
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
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  • 9
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    Genomic analysis of Thalassospira sp. SW-3-3 reveals its genetic potential for phthalate pollution remediation
    Elsevier BV ; 2022
    In:  Marine Genomics Vol. 63 ( 2022-06), p. 100953-
    Details
    In: Marine Genomics, Elsevier BV, Vol. 63 ( 2022-06), p. 100953-
    Type of Medium: Online Resource
    ISSN: 1874-7787
    URL: Article
    DOI: 10.1016/j.margen.2022.100953
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2022
    detail.hit.zdb_id: 2429626-0
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  • 10
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    TCA cycle enhancement and uptake of monomeric substrates support growth of marine Roseobacter at low temperature
    Springer Science and Business Media LLC ; 2022
    In:  Communications Biology Vol. 5, No. 1 ( 2022-07-14)
    Details
    In: Communications Biology, Springer Science and Business Media LLC, Vol. 5, No. 1 ( 2022-07-14)
    Abstract: Members of the marine Roseobacter group are ubiquitous in global oceans, but their cold-adaptive strategies have barely been studied. Here, as represented by Loktanella salsilacus strains enriched in polar regions, we firstly characterized the metabolic features of a cold-adapted Roseobacter by multi-omics, enzyme activities, and carbon utilization procedures. Unlike in most cold-adapted microorganisms, the TCA cycle is enhanced by accumulating more enzyme molecules, whereas genes for thiosulfate oxidation, sulfate reduction, nitrate reduction, and urea metabolism are all expressed at lower abundance when L. salsilacus was growing at 5 °C in comparison with higher temperatures. Moreover, a carbon-source competition experiment has evidenced the preferential use of glucose rather than sucrose at low temperature. This selective utilization is likely to be controlled by the carbon source uptake and transformation steps, which also reflects an economic calculation balancing energy production and functional plasticity. These findings provide a mechanistic understanding of how a Roseobacter member and possibly others as well counteract polar constraints.
    Type of Medium: Online Resource
    ISSN: 2399-3642
    URL: Article
    DOI: 10.1038/s42003-022-03631-2
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2919698-X
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