1
|
You XY, Liu JH, Tian H, Ding Y, Bu QY, Zhang KX, Ren GY, Duan X. Mucilaginibacter Phenanthrenivorans sp. nov., a Novel Phenanthrene Degradation Bacterium Isolated from Wetland Soil. Curr Microbiol 2022; 79:382. [DOI: 10.1007/s00284-022-03085-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/09/2022] [Indexed: 11/06/2022]
|
2
|
López GD, Álvarez-Rivera G, Carazzone C, Ibáñez E, Leidy C, Cifuentes A. Bacterial Carotenoids: Extraction, Characterization, and Applications. Crit Rev Anal Chem 2021; 53:1239-1262. [PMID: 34915787 DOI: 10.1080/10408347.2021.2016366] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Natural carotenoids are secondary metabolites that exhibit antioxidant, anti-inflammatory, and anti-cancer properties. These types of compounds are highly demanded by pharmaceutical, cosmetic, nutraceutical, and food industries, leading to the search for new natural sources of carotenoids. In recent years, the production of carotenoids from bacteria has become of great interest for industrial applications. In addition to carotenoids with C40-skeletons, some bacteria have the ability to synthesize characteristic carotenoids with C30-skeletons. In this regard, a great variety of methodologies for the extraction and identification of bacterial carotenoids has been reported and this is the first review that condenses most of this information. To understand the diversity of carotenoids from bacteria, we present their biosynthetic origin in order to focus on the methodologies employed in their extraction and characterization. Special emphasis has been made on high-performance liquid chromatography-mass spectrometry (HPLC-MS) for the analysis and identification of bacterial carotenoids. We end up this review showing their potential commercial use. This review is proposed as a guide for the identification of these metabolites, which are frequently reported in new bacteria strains.
Collapse
Affiliation(s)
- Gerson-Dirceu López
- Chemistry Department, Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Universidad de los Andes, Bogotá, Colombia
- Physics Department, Laboratory of Biophysics, Universidad de los Andes, Bogotá, Colombia
- Laboratory of Foodomics, Institute of Food Science Research (CIAL), CSIC, Madrid, Spain
| | | | - Chiara Carazzone
- Chemistry Department, Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Universidad de los Andes, Bogotá, Colombia
| | - Elena Ibáñez
- Laboratory of Foodomics, Institute of Food Science Research (CIAL), CSIC, Madrid, Spain
| | - Chad Leidy
- Physics Department, Laboratory of Biophysics, Universidad de los Andes, Bogotá, Colombia
| | - Alejandro Cifuentes
- Laboratory of Foodomics, Institute of Food Science Research (CIAL), CSIC, Madrid, Spain
| |
Collapse
|
3
|
Isolation, Characterization, and Antibiofilm Activity of Pigments Synthesized by Rhodococcus sp. SC1. Curr Microbiol 2021; 79:15. [PMID: 34905097 DOI: 10.1007/s00284-021-02694-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 10/12/2021] [Indexed: 10/19/2022]
Abstract
Infections from multi-drug resistant bacteria and biofilms constitute a serious problem worldwide. There is a need for new antibacterial and antibiofilm compounds in the fight against infectious diseases. In recent years, pigment-producing microorganisms have drawn a great deal of attention as a promising source for antibacterial and antibiofilm compounds. Here, we report the antibacterial and antibiofilm activity of pigments synthesized by bacteria isolated from soil. This study aimed to perform an evaluation of the antibacterial, antibiofilm, and characteristic of crude pigments from Rhodococcus sp. SC1 isolates. The total pigment extract exhibited antibacterial activity against Gram-positive and Gram-negative reference bacteria with required minimum inhibitory concentration (MIC) values ranging from 64 to 256 µg/ml. Moreover, it reduced biofilm formation of Gram-negative reference bacteria at sub-MIC concentration. For characterization of the pigments, UV-absorbance, thin layer chromatography, fourier transform infrared spectroscopy, and QTOF-LC/MS analyses were performed. The results of this study showed that pigments of Rhodococcus sp. SC1 isolates can be a candidate for medical applications.
Collapse
|
4
|
Xie F, Pei S, Huang X, Wang L, Kou J, Zhang G. Microcella flavibacter sp. nov., isolated from marine sediment, and reclassification of Chryseoglobus frigidaquae, Chryseoglobus indicus, and Yonghaparkia alkaliphila as Microcella frigidaquae comb. nov., Microcella indica nom. nov., and Microcella alkalica nom. nov. Antonie van Leeuwenhoek 2021; 114:2133-2145. [PMID: 34628559 DOI: 10.1007/s10482-021-01668-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 09/29/2021] [Indexed: 10/20/2022]
Abstract
A novel Gram-staining positive, aerobic, rod-shaped, non-motile and yellow-pigmented actinobacterium, designated strain WY83T, was isolated from a marine sediment of Indian Ocean. Strain WY83T grew optimally at 30-35 °C, pH 7-8 and with 0-3% (w/v) NaCl. The predominant menaquinones were MK-10, MK-11 and MK-12, and the major fatty acids were C19:1 ω9c/C19:1 ω11c, anteiso-C15:0, C17:0 3OH, and iso-C16:0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid. The cell-wall peptidoglycan contained lysine as a diamino acid. The DNA G + C content was 72.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and ninety-two bacterial core genes indicated that strain WY83T formed an evolutionary lineage with Chryseoglobus frigidaquae JCM 14730T, Chryseoglobus indicus CTD02-10-2T, Yonghaparkia alkaliphila JCM 15138T, Microcella alkaliphila DSM 18851T and Microcella putealis DSM 19627T within the radiation enclosing members of the family Microbacteriaceae. All pairwise percentage of conserved proteins between strain WY83T and the closely related phylogenetic neighbors were greater than 65%. The average nucleotide identity and in silico DNA-DNA hybridization values were both below the thresholds used for the delineation of a new species. On the basis of the evidence presented, strains WY83T, Y. alkaliphila JCM 15138T, C. frigidaquae JCM 14730T, M. alkaliphila DSM 18851T and M. putealis DSM 19627T should belong to different species of the same genus. Strain WY83T represents a novel species of the genus Microcella, for which the name Microcella flavibacter sp. nov. is proposed. The type strain is WY83T (= KCTC 39637T = MCCC 1A07099T). Furthermore, Chryseoglobus frigidaquae, Chryseoglobus indicus, and Yonghaparkia alkaliphila were reclassified as Microcella frigidaquae comb. nov., Microcella indica nom. nov., and Microcella alkalica nom. nov., respectively.
Collapse
Affiliation(s)
- Fuquan Xie
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, People's Republic of China
| | - Shengxiang Pei
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, People's Republic of China
| | - Xiaoyun Huang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, People's Republic of China
| | - Lina Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, People's Republic of China
| | - Jinyan Kou
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, People's Republic of China
| | - Gaiyun Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, People's Republic of China.
| |
Collapse
|
5
|
Brevibacterium limosum sp. nov., Brevibacterium pigmenatum sp. nov., and Brevibacterium atlanticum sp. nov., three novel dye decolorizing actinobacteria isolated from ocean sediments. J Microbiol 2021; 59:898-910. [PMID: 34491521 DOI: 10.1007/s12275-021-1235-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/14/2021] [Accepted: 07/21/2021] [Indexed: 10/20/2022]
Abstract
During a study of the marine actinobacterial biodiversity, a large number of Brevibacterium strains were isolated. Of these, five that have relatively low 16S rRNA gene similarity (98.5-99.3%) with validly published Brevibacterium species, were chosen to determine taxonomic positions. On the basis of 16S rRNA gene sequence analysis and BOX-PCR fingerprinting, strains o2T, YB235T, and WO024T were selected as representative strains. Genomic analyses, including average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), clearly differentiated the three strains from each other and from their closest relatives, with values ranging from 82.8% to 91.5% for ANI and from 26.7% to 46.5% for dDDH that below the threshold for species delineation. Strains YB235T, WO024T, and o2T all exhibited strong and efficient decolorization activity in congo red (CR) dyes, moderate decolorization activity in toluidine blue (TB) dyes and poor decolorization in reactive blue (RB) dyes. Genes coding for peroxidases and laccases were identified and accounted for these strains' ability to effectively oxidize a variety of dyes with different chemical structures. Mining of the whole genome for secondary metabolite biosynthesis gene clusters revealed the presence of gene clusters encoding for bacteriocin, ectoine, NRPS, siderophore, T3PKS, terpene, and thiopeptide. Based on the phylogenetic, genotypic and phenotypic data, strains o2T, YB235T and WO024T clearly represent three novel taxa within the genus Brevibacterium, for which the names Brevibacterium limosum sp. nov. (type strain o2T = JCM 33844T = MCCC 1A09961T), Brevibacterium pigmenatum sp. nov. (type strain YB235T = JCM 33843T = MCCC 1A09842T) and Brevibacterium atlanticum sp. nov. (type strain WO024T = JCM 33846T = MCCC 1A16743T) are proposed.
Collapse
|
6
|
Genomics- and Metabolomics-Based Investigation of the Deep-Sea Sediment-Derived Yeast, Rhodotorula mucilaginosa 50-3-19/20B. Mar Drugs 2020; 19:md19010014. [PMID: 33396687 PMCID: PMC7823890 DOI: 10.3390/md19010014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/14/2020] [Accepted: 12/24/2020] [Indexed: 01/10/2023] Open
Abstract
Red yeasts of the genus Rhodotorula are of great interest to the biotechnological industry due to their ability to produce valuable natural products, such as lipids and carotenoids with potential applications as surfactants, food additives, and pharmaceuticals. Herein, we explored the biosynthetic potential of R. mucilaginosa 50-3-19/20B collected from the Mid-Atlantic Ridge using modern genomics and untargeted metabolomics tools. R. mucilaginosa 50-3-19/20B exhibited anticancer activity when grown on PDA medium, while antimicrobial activity was observed when cultured on WSP-30 medium. Applying the bioactive molecular networking approach, the anticancer activity was linked to glycolipids, namely polyol esters of fatty acid (PEFA) derivatives. We purified four PEFAs (1–4) and the known methyl-2-hydroxy-3-(1H-indol-2-yl)propanoate (5). Their structures were deduced from NMR and HR-MS/MS spectra, but 1–5 showed no anticancer activity in their pure form. Illumina-based genome sequencing, de novo assembly and standard biosynthetic gene cluster (BGC) analyses were used to illustrate key components of the PEFA biosynthetic pathway. The fatty acid producing BGC3 was identified to be capable of producing precursors of PEFAs. Some Rhodotorula strains are able to convert inulin into high-yielding PEFA and cell lipid using a native exo-inulinase enzyme. The genomic locus for an exo-inulinase enzyme (g1629.t1), which plays an instrumental role in the PEFA production via the mannitol biosynthesis pathway, was identified. This is the first untargeted metabolomics study on R. mucilaginosa providing new genomic insights into PEFA biosynthesis.
Collapse
|
7
|
Pei S, Xie F, Wang W, Zhang S, Zhang G. Chryseoglobus indicus sp. nov., isolated from deep sea water. Int J Syst Evol Microbiol 2020; 71. [PMID: 33185523 DOI: 10.1099/ijsem.0.004564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, motile, aerobic, non-spore-forming and slender rod-shaped actinobacterium, designated strain CTD02-10-2T, was isolated from deep sea water of the Indian Ocean. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CTD02-10-2T was grouped into a separated branch with Chryseoglobus frigidaquae JCM 14730T (98.4 % nucleotide sequence identity). The respiratory quinones were menaquinones with 11, 12, 13 and 14 isoprene units and anteiso-C15 : 0, iso-C16 : 0, anteiso-C15 : 1 A and anteiso-C17 : 0 were the major fatty acids. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and three unknown glycolipids. The genome of strain CTD02-10-2T was 2.59 Mb, with a DNA G+C content of 69.6 mol% and contained genes involved in the biosynthesis of alkylresorcinol, ansamycin, and carotenoids. In silico DNA-DNA hybridization and average nucleotide identity values for whole-genome sequence comparisons between strain CTD02-10-2T and C. frigidaquae JCM 14730T were clearly below the thresholds used for the delineation of a new species. Based on its morphological and chemotaxonomic characteristics, as well as genotypic data, strain CTD02-10-2T was classified as a novel species of the genus Chryseoglobus, for which the name Chryseoglobus indicus sp. nov. is proposed. The type strain is CTD02-10-2T (=JCM 33842T=MCCC 1A16619T).
Collapse
Affiliation(s)
- Shengxiang Pei
- State Key Laboratory of Marine Environmental Science, College of Ocean and EarthSciences, Xiamen University, Xiamen 361102, Fujian, PR China.,Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| | - Fuquan Xie
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| | - Wenjing Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| | - Shuang Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| | - Gaiyun Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| |
Collapse
|
8
|
Pei S, Xie F, Niu S, Ma L, Zhang R, Zhang G. Brevibacterium profundi sp. nov., isolated from deep-sea sediment of the Western Pacific Ocean. Int J Syst Evol Microbiol 2020; 70:5818-5823. [DOI: 10.1099/ijsem.0.004483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A new Gram-stain-positive, aerobic, non-motile and rod-shaped actinobacterium, designated O1T, was isolated from a deep-sea sediment of the Western Pacific Ocean. Strain O1T showed optimal growth at 30 °C, between pH 6.0 and 8.0, and in the presence of 1–5 % (w/v) NaCl. The predominant menaquinone was MK-8 (H2), and anteiso-C15 : 0 and anteiso-C17 : 0 were the major fatty acids. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and one unknown glycolipid. The DNA G+C content of strain O1T was 64.9 mol% and the genome size was 4.17 Mb. Based on a similarity search and phylogenetic analysis of the 16S rRNA gene sequence, strain O1T belonged to the genus
Brevibacterium
. The values of average nucleotide identity and in silico DNA–DNA hybridization between strain O1T and its close relatives were well below the thresholds used for the delineation of a new species. On the basis of the morphological and chemotaxonomic characteristics, as well as the genotypic data, it is proposed that strain O1T represents a novel species of the genus
Brevibacterium
, for which the name Brevibacterium profundi sp. nov. is proposed. The type strain is O1T (=JCM 33845T=MCCC 1A16744T).
Collapse
Affiliation(s)
- Shengxiang Pei
- State Key Laboratory of Marine Environmental Science, College of Ocean and EarthSciences, Xiamen University, Xiamen 361102, Fujian, PR China
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| | - Fuquan Xie
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| | - Siwen Niu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| | - Lingqi Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and EarthSciences, Xiamen University, Xiamen 361102, Fujian, PR China
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| | - Rui Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080, PR China
- State Key Laboratory of Marine Environmental Science, College of Ocean and EarthSciences, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Gaiyun Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| |
Collapse
|
9
|
Wilhelm RC, Cyle KT, Martinez CE, Karasz DC, Newman JD, Buckley DH. Paraburkholderia solitsugae sp. nov. and Paraburkholderia elongata sp. nov., phenolic acid-degrading bacteria isolated from forest soil and emended description of Paraburkholderia madseniana. Int J Syst Evol Microbiol 2020; 70:5093-5105. [PMID: 32809929 DOI: 10.1099/ijsem.0.004387] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Two bacterial strains, 1NT and 5NT, were isolated from hemlock forest soil using a soluble organic matter enrichment. Cells of 1NT (0.65×1.85 µm) and 5NT (0.6×1.85 µm) are Gram-stain-negative, aerobic, motile, non-sporulating and exist as single rods, diplobacilli or in chains of varying length. During growth in dilute media (≤0.1× tryptic soy broth; TSB), cells are primarily motile with flagella. At higher concentrations (≥0.3× TSB), cells of both strains increasingly form non-motile chains, and cells of 5NT elongate (0.57×~7 µm) and form especially long filaments. Optimum growth of 1NT and 5NT occurred at 25-30 °C, pH 6.5-7.0 and <0.5% salinity. Results of comparative chemotaxonomic, genomic and phylogenetic analyses revealed that 1NT and 5NT were distinct from one another and their closest related type strains: Paraburkholderia madseniana RP11T, Paraburkholderia aspalathi LMG 27731T and Paraburkholderia caffeinilytica CF1T. The genomes of 1NT and 5NT had an average nucleotide identity (91.6 and 91.3%) and in silico DNA-DNA hybridization values (45.8%±2.6 and 45.5%±2.5) and differed in functional gene content from their closest related type strains. The composition of fatty acids and patterns of substrate use, including the catabolism of phenolic acids, also differentiated strains 1NT and 5NT from each other and their closest relatives. The only ubiquinone present in strains 1NT and 5NT was Q-8. The major cellular fatty acids were C16 : 0, 3OH-C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c and summed features 2 (3OH-C14 : 0 / C16 : 1 iso I), 3 (C16 : 1 ω6c/ω7c) and 8 (C18 : 1 ω7c/ω6c). A third bacterium, strain RL16-012-BIC-B, was isolated from soil associated with shallow roots and was determined to be a strain of P. madseniana (ANI, 98.8%; 16S rRNA gene similarity, 100%). Characterizations of strain RL16-012-BIC-B (DSM 110723=LMG 31706) led to proposed emendments to the species description of P. madseniana. Our polyphasic approach demonstrated that strains 1NT and 5NT represent novel species from the genus Paraburkholderia for which the names Paraburkholderia solitsugae sp. nov. (type strain 1NT=DSM 110721T=LMG 31704T) and Paraburkholderia elongata sp. nov. (type strain 5NT=DSM 110722T=LMG 31705T) are proposed.
Collapse
Affiliation(s)
- Roland C Wilhelm
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - K Taylor Cyle
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Carmen Enid Martinez
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - David C Karasz
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | | | - Daniel H Buckley
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| |
Collapse
|
10
|
Zhou Y, Pei S, Xie F, Gu L, Zhang G. Saccharopolyspora coralli sp. nov. a novel actinobacterium isolated from the stony coral Porites. Int J Syst Evol Microbiol 2020; 70:3241-3246. [PMID: 32375933 DOI: 10.1099/ijsem.0.004162] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, aerobic, non-motile actinobacterium, designated strain E2AT, was isolated from a coral sample and examined using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain E2AT formed a distinct phyletic lineage in the genus Saccharopolyspora and was closely related to S. cavernae CCTCC AA 2012022T (96.4 %) and S. lacisalsi CCTCC AA 2010012T (95.3 %). The isolate grew at 15-35 °C, pH 5-12 and in the presence of 1-16 % (w/v) NaCl. The cell-wall diamino acid was meso-DAP. Major fatty acids identified were iso-C15 : 0, iso-C16 : 0 and C17 : 1 ω8c. The predominant menaquinone was MK-9(H4). The polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmethylethanolamine, one unidentified glycolipid, one unidentified phospholipid and one unidentified aminolipid. The genomic DNA G+C content was 68.6 mol%. Based on the data from the polyphasic taxonomic study reported here, strain E2AT represents a novel species within the genus Saccharopolyspora, for which the name Saccharopolyspora coralli sp. nov. is proposed. The type strain is E2AT=(JCM 31844T=MCCC 1A17150T).
Collapse
Affiliation(s)
- Yuan Zhou
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| | - Shengxiang Pei
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| | - Fuquan Xie
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| | - Li Gu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| | - Gaiyun Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| |
Collapse
|
11
|
Aldana J, Romero-Otero A, Cala MP. Exploring the Lipidome: Current Lipid Extraction Techniques for Mass Spectrometry Analysis. Metabolites 2020; 10:metabo10060231. [PMID: 32503331 PMCID: PMC7345237 DOI: 10.3390/metabo10060231] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/05/2020] [Accepted: 05/13/2020] [Indexed: 12/14/2022] Open
Abstract
In recent years, high-throughput lipid profiling has contributed to understand the biological, physiological and pathological roles of lipids in living organisms. Across all kingdoms of life, important cell and systemic processes are mediated by lipids including compartmentalization, signaling and energy homeostasis. Despite important advances in liquid chromatography and mass spectrometry, sample extraction procedures remain a bottleneck in lipidomic studies, since the wide structural diversity of lipids imposes a constrain in the type and amount of lipids extracted. Differences in extraction yield across lipid classes can induce a bias on down-stream analysis and outcomes. This review aims to summarize current lipid extraction techniques used for untargeted and targeted studies based on mass spectrometry. Considerations, applications, and limitations of these techniques are discussed when used to extract lipids in complex biological matrices, such as tissues, biofluids, foods, and microorganisms.
Collapse
|
12
|
Hrichi S, Chaabane-Banaoues R, Giuffrida D, Mangraviti D, Oulad El Majdoub Y, Rigano F, Mondello L, Babba H, Mighri Z, Cacciola F. Effect of seasonal variation on the chemical composition and antioxidant and antifungal activities of Convolvulus althaeoides L. leaf extracts. ARAB J CHEM 2020. [DOI: 10.1016/j.arabjc.2020.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
|
13
|
Wilhelm RC, Murphy SJL, Feriancek NM, Karasz DC, DeRito CM, Newman JD, Buckley DH. Paraburkholderia madseniana sp. nov., a phenolic acid-degrading bacterium isolated from acidic forest soil. Int J Syst Evol Microbiol 2020; 70:2137-2146. [PMID: 32027304 DOI: 10.1099/ijsem.0.004029] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
RP11T was isolated from forest soil following enrichment with 4-hydroxybenzoic acid. Cells of RP11T are aerobic, non-sporulating, exhibit swimming motility, and are rods (0.8 µm by 1.4 µm) that often occur as diplobacillus or in short chains (3-4 cells). Optimal growth on minimal media containing 4-hydroxybenzoic acid (µ=0.216 hr-1) occurred at 30 °C, pH 6.5 or 7.0 and 0% salinity. Comparative chemotaxonomic, genomic and phylogenetic analyses revealed the isolate was distinct from its closest relative type strains identified as Paraburkholderia aspalathi LMG 27731T, Paraburkholderia fungorum LMG 16225T and Paraburkholderia caffeinilytica CF1T. Strain RP11T is genetically distinct from P. aspalathi, its closest relative, in terms of 16S rRNA gene sequence similarity (98.7%), genomic average nucleotide identity (94%) and in silico DNA-DNA hybridization (56.7 %±2.8). The composition of fatty acids and substrate utilization pattern differentiated strain RP11T from its closest relatives, including growth on phthalic acid. Strain RP11T encoded the greatest number of aromatic degradation genes of all eleven closely related type strains and uniquely encoded a phthalic acid dioxygenase and paralog of the 3-hydroxybenzoate 4-monooxygenase. The only ubiquinone detected in strain RP11T was Q-8, and the major cellular fatty acids were C16 : 0, 3OH-C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c, and summed feature 8 (C18 : 1 ω7c/ω6c). On the basis of this polyphasic approach, it was determined that strain RP11T represents a novel species from the genus Paraburkholderia for which the name Paraburkholderia madseniana sp. nov. is proposed. The type strain is RP11T (=DSM 110123T=LMG 31517T).
Collapse
Affiliation(s)
- Roland C Wilhelm
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Sean J L Murphy
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Nicole M Feriancek
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - David C Karasz
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Christopher M DeRito
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY, 14853, USA
| | | | - Daniel H Buckley
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| |
Collapse
|
14
|
Zhang G, Wang L, Xie F, Pei S, Jiang L. Nesterenkonia salmonea sp. nov. and Nesterenkonia sphaerica sp. nov., isolated from the Southern Atlantic Ocean. Int J Syst Evol Microbiol 2020; 70:923-928. [DOI: 10.1099/ijsem.0.003847] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Gaiyun Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| | - Lina Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| | - Fuquan Xie
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| | - Shengxiang Pei
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| | - Li Jiang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| |
Collapse
|
15
|
Wang X, He SW, Guo HB, Thin KK, Gao JS, Wang Y, Zhang XX. Pseudomonas rhizoryzae sp. nov., isolated from rice. Int J Syst Evol Microbiol 2019; 70:944-950. [PMID: 31751195 DOI: 10.1099/ijsem.0.003852] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two yellow-pigmented, Gram-stain-negative and rod-shaped bacterial strains, designated as RY24T and ZYY160, were isolated from rice. Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strains RY24T and ZYY160 belonged to the genus Pseudomonas, and the 16S rRNA gene sequence similarity was 100 % The DNA homology between the two strains was 99.7 %. The 16S rRNA and rpoD gene sequences of the two strains showed highest similarity values to Pseudomonas oryzihabitans CGMCC 1.3392T and Pseudomonas psychrotolerans DSM 15758T (sharing 99.31 and 94.34 %, respectively). The major fatty acids of two strains were identified as summed feature 8 (C18:1ω7c and/or C18:1ω6c), C16;0 and summed feature 3 (C16:1ω7c and/or C16:1ω6c), and the major respiratory quinone was identified as ubiquinone Q-9, which are typical chemotaxonomic features of members of the genus Pseudomonas. The genomic DNA G+C contents of strains RY24T and ZYY160 were determined to be 64.25 and 64.21 mol%, respectively. The DNA-DNA relatedness and average nucleotide identity values between the two strains and their closely related type strains were below 36 and 90 %, which supported that RY24T and ZYY160 represent a novel species in the genus Pseudomonas. Phylogenetic and chemotaxonomic evidence, together with phenotypic characteristics, showed that the two isolates constitute a novel species of the genus Pseudomonas. The type strain is RY24T (JCM 33201T=ACCC 61555T), for which the name Pseudomonas rhizoryzae sp. nov. is proposed.
Collapse
Affiliation(s)
- Xing Wang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Shan-Wen He
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
- College of Life Science, The Yangtze university, Jingzhou, 434025, PR China
| | - He-Bao Guo
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Kyu Kyu Thin
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Ju-Sheng Gao
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
- Qiyang Agro-ecosystem of National Field Experimental Station, Institute of Agricultural Resources and Regional, Chinese Academy of Agricultural Sciences, Qiyang 426182, PR China
| | - Yao Wang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
- College of Life Science, The Yangtze university, Jingzhou, 434025, PR China
| | - Xiao-Xia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| |
Collapse
|
16
|
Autenrieth C, Ghosh R. The Methoxylated, Highly Conjugated C 40 Carotenoids, Spirilloxanthin and Anhydrorhodovibrin, Can Be Separated Using High Performance Liquid Chromatography with Safe and Environmentally Friendly Solvents. Metabolites 2019; 9:metabo9020020. [PMID: 30682824 PMCID: PMC6410002 DOI: 10.3390/metabo9020020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/11/2019] [Accepted: 01/19/2019] [Indexed: 11/21/2022] Open
Abstract
High performance liquid chromatography (HPLC) is a frequently used technique in carotenoid research. So far, however, little attention has been paid to the fact that many of the organic solvents used in HPLC separation of highly apolar C40 carotenoids impose a significant threat to both health (especially for women) and the general laboratory environment. Here, we developed a solvent combination capable of allowing high-resolution HPLC separation of the C40 carotenoid, spirilloxanthin, and all of its biosynthetic precursors beginning with phytoene, using relatively safe, environmentally friendly solvents. We show that separation of spirilloxanthin and its precursors anhydrorhodovibrin and lycopene using modern ultra-high performance chromatography (UHPLC) poses particular problems for apolar carotenoid separation, due to the long residence times in the sample delivery system, which facilitates carotenoid aggregation. We resolved these problems by developing the solvent delivery combination acetone/acetonitrile/isopropanol/methanol (65/30/5/2 (v/v/v/v)), which allows excellent column separation using the safe isocratic solvent system methanol/tetrahydrofuran (98/2 (v/v)). We also demonstrate that the development strategy for optimizing a solvent system for carotenoid separation can be well-described by the use of the average dielectric constant of the total sample delivery solvent, and present a formal method for analysis of the efficiency of separation.
Collapse
Affiliation(s)
- Caroline Autenrieth
- Department of Bioenergetics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany.
| | - Robin Ghosh
- Department of Bioenergetics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany.
| |
Collapse
|
17
|
Mucilaginibacter xinganensis sp. nov., a phenanthrene-degrading bacterium isolated from wetland soil. Antonie van Leeuwenhoek 2018; 112:641-649. [DOI: 10.1007/s10482-018-1194-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/20/2018] [Indexed: 10/28/2022]
|
18
|
Characterization of MK₈(H₂) from Rhodococcus sp. B7740 and Its Potential Antiglycation Capacity Measurements. Mar Drugs 2018; 16:md16100391. [PMID: 30340371 PMCID: PMC6213960 DOI: 10.3390/md16100391] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/23/2018] [Accepted: 10/11/2018] [Indexed: 12/18/2022] Open
Abstract
Menaquinone (MK) has an important role in human metabolism as an essential vitamin (VK2), which is mainly produced through the fermentation of microorganisms. MK8(H2) was identified to be the main menaquinone from Rhodococcus sp. B7740, a bacterium isolated from the arctic ocean. In this work, MK8(H2) (purity: 99.75%) was collected through a convenient and economic extraction process followed by high-speed countercurrent chromatography (HSCCC) purification. Additionally, high-resolution mass spectrometry (HRMS) was performed for further identification and the hydrogenation position of MK8(H2) (terminal unit) was determined using nuclear magnetic resonance (NMR) for the first time. MK8(H2) showed a superior antioxidant effect and antiglycation capacity compared with ubiquinone Q10 and MK4. High-performance liquid chromatography–mass spectrometer (HPLC-MS/MS) and molecular docking showed the fine interaction between MK8(H2) with methylglyoxal (MGO) and bull serum albumin (BSA), respectively. These properties make MK8(H2) a promising natural active ingredient with future food and medicine applications.
Collapse
|
19
|
Jedlińska K, Strus M, Baś B. A new electrochemical sensor with the Refreshable Silver Liquid Amalgam Film multi-Electrode for sensitive voltammetric determination of vitamin K2 (menaquinone). Electrochim Acta 2018. [DOI: 10.1016/j.electacta.2018.01.204] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
20
|
Antolak H, Oracz J, Otlewska A, Żyżelewicz D, Kręgiel D. Identification of Carotenoids and Isoprenoid Quinones from Asaia lannensis and Asaia bogorensis. Molecules 2017; 22:molecules22101608. [PMID: 28946700 PMCID: PMC6151773 DOI: 10.3390/molecules22101608] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 09/24/2017] [Accepted: 09/24/2017] [Indexed: 12/11/2022] Open
Abstract
The aim of the study was to identify and quantitatively assess of carotenoids and isoprenoid quinones biosynthesized by six different strains of acetic acid bacteria, belonging to genus Asaia, that are common beverage-spoiling bacteria in Europe. Bacterial cultures were conducted in a laboratory liquid culture minimal medium with 2% sucrose. Carotenoids and isoprenoid quinones were investigated using UHPLC-DAD-ESI-MS analysis. In general, tested strains of Asaia spp. were able to produce 10 carotenoids and 3 isoprenoid quinones: menaquinone-7, menaquinone-8, and ubiquinone-10. The main identified carotenoids in Asaia lannensis strains were phytofluene, neurosporene, α-carotene, while for Asaia bogorensis, neurosporene, canthaxanthin, and zeaxanthin were noted. What is more, tested Asaia spp. were able to produce myxoxanthophyll, which has so far been identified primarily in cyanobacteria. The results show that A. lannensis are characterized by statistically higher concentrations of produced carotenoids, as well as a greater variety of these compounds. We have noted that carotenoids were not only accumulated by bacterial cells, but also some strains of A. lannensis produced extracellular carotenoids.
Collapse
Affiliation(s)
- Hubert Antolak
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Science, Lodz University of Technology, 171/173 Wólczańska, 90-924 Lodz, Poland.
| | - Joanna Oracz
- Institute of Food Technology and Analysis, Faculty of Biotechnology and Food Science, Lodz University of Technology, 4/10 Stefanowskiego, 90-924 Lodz, Poland.
| | - Anna Otlewska
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Science, Lodz University of Technology, 171/173 Wólczańska, 90-924 Lodz, Poland.
| | - Dorota Żyżelewicz
- Institute of Food Technology and Analysis, Faculty of Biotechnology and Food Science, Lodz University of Technology, 4/10 Stefanowskiego, 90-924 Lodz, Poland.
| | - Dorota Kręgiel
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Science, Lodz University of Technology, 171/173 Wólczańska, 90-924 Lodz, Poland.
| |
Collapse
|
21
|
Chen Y, Xie B, Yang J, Chen J, Sun Z. Identification of microbial carotenoids and isoprenoid quinones from Rhodococcus sp. B7740 and its stability in the presence of iron in model gastric conditions. Food Chem 2017; 240:204-211. [PMID: 28946263 DOI: 10.1016/j.foodchem.2017.06.067] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/19/2017] [Accepted: 06/09/2017] [Indexed: 11/30/2022]
Abstract
Rhodococcus sp. B7740 is a newfound bacterium which was isolated from 25m deep seawater in the arctic. In this paper, Rhodococcus sp. B7740 was firstly discovered to produce abundant natural isoprenoids, including ubiquinone-4(UQ-4), 13 kinds of menaquinones, three rare aromatic carotenoids and more than one common carotenoid. These compounds were identified by UV-Visible, HPLC-APCI-MS/MS and HRMS spectra. Results demonstrated that Rhodococcus sp. B7740 might be a worthy source of natural isoprenoids especially for scarce aromatic carotenoids. Among them, isorenieratene with 528.3762Da (calculated for 528.3756Da, error: 1.1ppm), a carotenoid with aromatic ring, was purified by HSCCC. The stability of isorenieratene under the mimical gastric conditions was measured compared with common dietary carotenoids, β-carotene and lutein. Unlike β-carotene and lutein, isorenieratene exhibited rather stable in the presence of free iron or heme iron. Its high retention rate in gastrointestinal tract after ingestion indicates the benefits for health.
Collapse
Affiliation(s)
- Yashu Chen
- Natural Product Laboratory, Department of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China.
| | - Bijun Xie
- Natural Product Laboratory, Department of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Jifang Yang
- College of Biological and Environmental Science, Zhejiang Wanli University, Ningbo, Zhejiang 315100, People's Republic of China
| | - Jigang Chen
- College of Biological and Environmental Science, Zhejiang Wanli University, Ningbo, Zhejiang 315100, People's Republic of China
| | - Zhida Sun
- Natural Product Laboratory, Department of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China.
| |
Collapse
|
22
|
Zhang G, Wang L, Li J, Zhou Y. Pseudonocardia profundimaris sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2017; 67:1693-1697. [DOI: 10.1099/ijsem.0.001849] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Gaiyun Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China
| | - Lina Wang
- School of Biological Engineering, Qilu University of Technology, Jinana 250353, Shandong, PR China
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China
| | - Jinglong Li
- School of Biological Engineering, Qilu University of Technology, Jinana 250353, Shandong, PR China
| | - Yuan Zhou
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China
| |
Collapse
|
23
|
Zhang G, Wang L, Li J, Zhou Y. Amycolatopsis albispora sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2016; 66:3860-3864. [DOI: 10.1099/ijsem.0.001277] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Gaiyun Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, PR China
| | - Lina Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China
- School of Biological Engineering, Qilu University of Technology, Jinan 250353, Shandong, PR China
| | - Jinglong Li
- School of Biological Engineering, Qilu University of Technology, Jinan 250353, Shandong, PR China
| | - Yuan Zhou
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, PR China
| |
Collapse
|
24
|
Kellermann MY, Yoshinaga MY, Valentine RC, Wörmer L, Valentine DL. Important roles for membrane lipids in haloarchaeal bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2940-2956. [PMID: 27565574 DOI: 10.1016/j.bbamem.2016.08.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 08/11/2016] [Accepted: 08/19/2016] [Indexed: 10/21/2022]
Abstract
Recent advances in lipidomic analysis in combination with various physiological experiments set the stage for deciphering the structure-function of haloarchaeal membrane lipids. Here we focused primarily on changes in lipid composition of Haloferax volcanii, but also performed a comparative analysis with four other haloarchaeal species (Halobacterium salinarum, Halorubrum lacusprofundi, Halorubrum sodomense and Haloplanus natans) all representing distinctive cell morphologies and behaviors (i.e., rod shape vs. pleomorphic behavior). Common to all five haloarchaea, our data reveal an extraordinary high level of menaquinone, reaching up to 72% of the total lipids. This ubiquity suggests that menaquinones may function beyond their ordinary role as electron and proton transporter, acting simultaneously as ion permeability barriers and as powerful shield against oxidative stress. In addition, we aimed at understanding the role of cations interacting with the characteristic negatively charged surface of haloarchaeal membranes. We propose for instance that by bridging the negative charges of adjacent anionic phospholipids, Mg2+ acts as surrogate for cardiolipin, a molecule that is known to control curvature stress of membranes. This study further provides a bioenergetic perspective as to how haloarchaea evolved following oxygenation of Earth's atmosphere. The success of the aerobic lifestyle of haloarchaea includes multiple membrane-based strategies that successfully balance the need for a robust bilayer structure with the need for high rates of electron transport - collectively representing the molecular basis to inhabit hypersaline water bodies around the planet.
Collapse
Affiliation(s)
- Matthias Y Kellermann
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA.
| | - Marcos Y Yoshinaga
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Leobener Strasse, D-28359 Bremen, Germany
| | | | - Lars Wörmer
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Leobener Strasse, D-28359 Bremen, Germany
| | - David L Valentine
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA.
| |
Collapse
|
25
|
Altererythrobacter aurantiacus sp. nov., isolated from deep-sea sediment. Antonie van Leeuwenhoek 2016; 109:1245-51. [DOI: 10.1007/s10482-016-0726-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/27/2016] [Indexed: 10/21/2022]
|
26
|
Wang L, Li J, Zhang G. Nocardioides rotundus sp. nov., isolated from deep seawater. Int J Syst Evol Microbiol 2016; 66:1932-1936. [DOI: 10.1099/ijsem.0.000966] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Lina Wang
- School of Biological Engineering, Qilu University of Technology, Jinan 250353, Shandong, PR China
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China
| | - Jinglong Li
- School of Biological Engineering, Qilu University of Technology, Jinan 250353, Shandong, PR China
| | - Gaiyun Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China
| |
Collapse
|
27
|
Hyun DW, Jung MJ, Kim MS, Shin NR, Kim PS, Whon TW, Bae JW. Proteus cibarius sp. nov., a swarming bacterium from Jeotgal, a traditional Korean fermented seafood, and emended description of the genus Proteus. Int J Syst Evol Microbiol 2016; 66:2158-2164. [PMID: 26944634 DOI: 10.1099/ijsem.0.001002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Proteus-like, Gram-stain-negative, facultatively anaerobic, rod-shaped bacterium, designated strain JS9T, was isolated from Korean fermented seafood, Jeotgal. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain JS9T belonged to the genus Proteus in the family Enterobacteriaceae. The highest 16S rRNA gene sequence similarity of strain JS9T was to Proteus vulgaris KCTC 2579T (98.98 %) and the genomic DNA G+C content is 39.0 mol%. DNA-DNA hybridization values were measured and strain JS9T showed <20.8 % genomic relatedness with closely-related members of the genus Proteus. The isolate showed bacterial motility and swarming activity similar to those of pathogenic Proteus mirabilis but distinct from those of other species of the genus Proteus. The isolate grows optimally at 30 °C, at pH 7, and in the presence of 2 % (w/v) NaCl. The main respiratory quinones are ubiquinone Q-8 and Q-10, and the major cellular fatty acids are C16 : 0, summed feature 3 and summed feature 8. The polar lipids comprise phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unidentified amino lipid, two unidentified amino-phospholipids, and three unidentified lipids. Based on phylogenetic, phenotypic, chemotaxonomic and genotypic analyses, strain JS9T represents a novel species of the genus Proteus, for which the name Proteus cibarius sp. nov. is proposed. The type strain is JS9T (=KACC 18404T=JCM 30699T). An emended description of the genus Proteus is also provided.
Collapse
Affiliation(s)
- Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea
| | - Mi-Ja Jung
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea
| | - Min-Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea
| | - Pil Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea
| | - Tae Woong Whon
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Republic of Korea
| |
Collapse
|
28
|
Zhang G, Wang S, Wang L. Sediminivirga luteola gen. nov., sp. nov., a member of the family Brevibacteriaceae, isolated from marine sediment. Int J Syst Evol Microbiol 2016; 66:1494-1498. [PMID: 26791052 DOI: 10.1099/ijsem.0.000909] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive actinobacterial strain, designated F23T, was isolated from marine sediment collected from the western Pacific. Strain F23T showed less than 94.5 % 16S rRNA gene sequence similarity with type strains of species with validly published names. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that the novel isolate formed a distinct monophyletic clade within the family Brevibacteriaceae and clustered distantly with the genera Brevibacterium and Spelaeicoccus. Cells of strain F23T were non-motile, rod-shaped and aerobic to microaerophilic. Optimal growth occurred at 35-37 °C, at pH 8.0-9.0 and in the presence of 1 % NaCl (w/v). The isolate contained meso-diaminopimelic acid as the characteristic cell-wall diamino acid, MK-8(H2) and MK-7(H2) as the predominant menaquinones and anteiso-C15 : 0 and anteiso-C17 : 0 as the major fatty acids. The DNA G+C content of strain F23T was 69.0 mol%. On the basis of phylogenetic analysis, phenotypic and chemotaxonomic characteristics and 16S rRNA gene signature nucleotide patterns, strain F23T represents a novel species in a novel genus in the family Brevibacteriaceae, for which the name Sediminivirga luteola gen. nov., sp. nov. is proposed. The type strain is F23T ( = JCM 19771T = CGMCC 1.12785T = MCCC 1A09945T).
Collapse
Affiliation(s)
- Gaiyun Zhang
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China.,Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China
| | - Shuang Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China
| | - Lina Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China
| |
Collapse
|
29
|
Calegari-Santos R, Diogo RA, Fontana JD, Bonfim TMB. Carotenoid Production by Halophilic Archaea Under Different Culture Conditions. Curr Microbiol 2016; 72:641-51. [PMID: 26750123 DOI: 10.1007/s00284-015-0974-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 11/22/2015] [Indexed: 12/16/2022]
Abstract
Carotenoids are pigments that may be used as colorants and antioxidants in food, pharmaceutical, and cosmetic industries. Since they also benefit human health, great efforts have been undertaken to search for natural sources of carotenoids, including microbial ones. The optimization of culture conditions to increase carotenoid yield is one of the strategies used to minimize the high cost of carotenoid production by microorganisms. Halophilic archaea are capable of producing carotenoids according to culture conditions. Their main carotenoid is bacterioruberin with 50 carbon atoms. In fact, the carotenoid has important biological functions since it acts as cell membrane reinforcement and it protects the microorganism against DNA damaging agents. Moreover, carotenoid extracts from halophilic archaea have shown high antioxidant capacity. Therefore, current review summarizes the effect of different culture conditions such as salt and carbon source concentrations in the medium, light incidence, and oxygen tension on carotenoid production by halophilic archaea and the strategies such as optimization methodology and two-stage cultivation already used to increase the carotenoid yield of these microorganisms.
Collapse
Affiliation(s)
- Rossana Calegari-Santos
- Department of Pharmacy, Enzymology and Fermentation Technology Laboratory, Federal University of Paraná, Av. Pref. Lothário Meissner, 632, Curitiba, Paraná, 80210-170, Brazil
| | - Ricardo Alexandre Diogo
- Polytechnic School, Control and Automation Engineering, Pontifical Catholic University of Paraná, Rua Imaculada Conceição, 1155, Curitiba, Paraná, 80215-901, Brazil
| | - José Domingos Fontana
- Department of Chemistry and Biology, Federal Technological University of Paraná, Rua Deputado Heitor Alencar Furtado, 5000, Curitiba, Paraná, 81280-340, Brazil
| | - Tania Maria Bordin Bonfim
- Department of Pharmacy, Enzymology and Fermentation Technology Laboratory, Federal University of Paraná, Av. Pref. Lothário Meissner, 632, Curitiba, Paraná, 80210-170, Brazil.
| |
Collapse
|
30
|
Elling FJ, Becker KW, Könneke M, Schröder JM, Kellermann MY, Thomm M, Hinrichs KU. Respiratory quinones in Archaea: phylogenetic distribution and application as biomarkers in the marine environment. Environ Microbiol 2015; 18:692-707. [PMID: 26472620 DOI: 10.1111/1462-2920.13086] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 07/28/2015] [Accepted: 10/10/2015] [Indexed: 11/30/2022]
Abstract
The distribution of respiratory quinone electron carriers among cultivated organisms provides clues on both the taxonomy of their producers and the redox processes these are mediating. Our study of the quinone inventories of 25 archaeal species belonging to the phyla Eury-, Cren- and Thaumarchaeota facilitates their use as chemotaxonomic markers for ecologically important archaeal clades. Saturated and monounsaturated menaquinones with six isoprenoid units forming the alkyl chain may serve as chemotaxonomic markers for Thaumarchaeota. Other diagnostic biomarkers are thiophene-bearing quinones for Sulfolobales and methanophenazines as functional quinone analogues of the Methanosarcinales. The ubiquity of saturated menaquinones in the Archaea in comparison to Bacteria suggests that these compounds may represent an ancestral and diagnostic feature of the Archaea. Overlap between quinone compositions of distinct thermophilic and halophilic archaea and bacteria may indicate lateral gene transfer. The biomarker potential of thaumarchaeal quinones was exemplarily demonstrated on a water column profile of the Black Sea. Both, thaumarchaeal quinones and membrane lipids showed similar distributions with maxima at the chemocline. Quinone distributions indicate that Thaumarchaeota dominate respiratory activity at a narrow interval in the chemocline, while they contribute only 9% to the microbial biomass at this depth, as determined by membrane lipid analysis.
Collapse
Affiliation(s)
- Felix J Elling
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Kevin W Becker
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Martin Könneke
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Jan M Schröder
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Matthias Y Kellermann
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA, 93106, USA
| | - Michael Thomm
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, 93053, Regensburg, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| |
Collapse
|
31
|
Hyun DW, Oh SJ, Kim MS, Whon TW, Jung MJ, Shin NR, Kim PS, Kim HS, Lee JY, Kang W, Bae JW. Simplicispira piscis sp. nov., isolated from the gut of a Korean rockfish, Sebastes schlegelii. Int J Syst Evol Microbiol 2015; 65:4689-4694. [DOI: 10.1099/ijsem.0.000635] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic, motile and rod-shaped bacterium, designated strain RSG39T, was isolated from the gut of a Korean rockfish, Sebastes schlegelii. The 16S rRNA gene sequence analysis revealed that strain RSG39T belonged to the genus Simplicispira in the class Betaproteobacteria and its highest sequence similarity was shared with S. psychrophila (98.4 %). The isolate grew optimally at 20 °C, at pH 7 and with 0 % (w/v) NaCl. The main respiratory quinone of the isolate was ubiquinone Q-8. The major cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The polar lipids of the isolate were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and six unidentified lipids. The DNA–DNA hybridization values showed < 7.4 % genomic relatedness with closely related strains. The genomic DNA G+C content was 65.2 mol %. Based on phylogenetic, phenotypic, chemotaxonomic and genotypic analyses, strain RSG39T represents a novel species of the genus Simplicispira, for which the name Simplocospira piscis sp. nov. is proposed. The type strain is RSG39T ( = KACC 17539T = JCM 19291T).
Collapse
Affiliation(s)
- Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Sei Joon Oh
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Min-Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Tae Woong Whon
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Mi-Ja Jung
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Pil Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Hyun Sik Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - June-Young Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Woorim Kang
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| |
Collapse
|
32
|
Hyun DW, Kim JY, Kim MS, Shin NR, Kim HS, Lee JY, Bae JW. Actibacter haliotis sp. nov., isolated from the gut of an abalone, Haliotis discus hannai, and emended description of the genus Actibacter. Int J Syst Evol Microbiol 2015; 65:49-55. [DOI: 10.1099/ijs.0.067041-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strain, designated strain W113T, was isolated from the gut of an abalone, Haliotis discus hannai, which was collected from the northern coast of Jeju in Korea. The isolate was a Gram-staining-negative, facultatively anaerobic, non-motile, rod-shaped bacterium producing yellow-to-orange carotenoid-type pigments. 16S rRNA gene sequence analysis showed that the isolate belonged to the genus
Actibacter
in the family
Flavobacteriaceae
and it shared the highest sequence similarity with the type strain of
Actibacter sediminis
(98.8 % similarity). Optimal growth occurred at 25 °C, at pH 7 and with 2 % (w/v) NaCl. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C15 : 1 G. Menaquinone-6 was the main respiratory quinone. The polar lipids of the isolate were phosphatidylethanolamine, three unidentified amino lipids, and three unidentified lipids. The genomic DNA G+C content was 42.6 mol% and DNA–DNA hybridization values indicated that the strain shared <18 % genomic relatedness with the most closely related species. The results of the phylogenetic, phenotypic and genotypic analyses indicated that strain W113T represents a novel species in the genus
Actibacter
, for which the name Actibacter haliotis sp. nov. is proposed. The type strain is W113T ( = KACC 17209T = JCM 18868T).
Collapse
Affiliation(s)
- Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Joon Yong Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Min-Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Hyun Sik Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - June-Young Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| |
Collapse
|
33
|
Citrimicrobium luteum gen. nov., sp. nov., aerobic anoxygenic phototrophic bacterium isolated from the gut of a sea cucumber Stichopus japonicus. J Microbiol 2014; 52:819-24. [PMID: 25163838 DOI: 10.1007/s12275-014-4136-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 07/17/2014] [Accepted: 08/05/2014] [Indexed: 10/24/2022]
Abstract
A Gram-stain negative, yellow-pigmented, motile, pleomorphic bacterium, designated strain CBA4602(T), was isolated from the gut of the sea cucumber Stichopus japonicus, which was collected from Jeju Island in the Republic of Korea. In a phylogenetic analysis based on the 16S rRNA gene, strain CBA4602(T) belonged to the order Sphingomonadales in the class Alphaproteobacteria. The 16S rRNA gene sequence similarity between strain CBA4602(T) and 'Citromicrobium bathyomarinum' JF-1, the most closely related strain having nonvalidly published name, was 98.4%, followed by 95.2-96.7% identities with sequence of the other closest strains in the genus Erythrobacter. Strain CBA4602(T) had bacteriochlorophyll a and carotenoids. Strain CBA4602(T) grew in 0-10% (w/v) NaCl, at 10-42°C and pH 6.0-8.0, with optimal growth in 1-2% NaCl, at 30-37°C and pH 7.0. Strain CBA4602(T) was positive for catalase and oxidase activities and was able to hydrolyse gelatine and Tween 20 and 40, but not starch, Tween 80 or L-tyrosine. The G+C content of genomic DNA from strain CBA4602(T) was 68.0 mol% and Q-10 was the major detected isoprenoid quinone. The polar lipids were three unidentified phospholipids, three unidentified glycolipids, and two unidentified lipids. The dominant fatty acids were anteiso-C15:0, C16:0, anteiso-C17:0 and C18:0. As considering the current taxonomic status of the genus 'Citromicrobium' and polyphasic taxonomic analyses, strain CBA4602(T) represents a novel genus and species. The name Citrimicrobium luteum is proposed for the type strain CBA4602(T) (=KACC 17668(T) =JCM 19530(T)).
Collapse
|
34
|
Fan X, Zhang Z, Li Z, Zhang XH. Luteococcus
sediminum sp. nov., isolated from deep subseafloor sediment of the South Pacific Gyre. Int J Syst Evol Microbiol 2014; 64:2522-2527. [DOI: 10.1099/ijs.0.058529-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
A Gram-stain-positive, strictly aerobic, coccus-shaped, non-motile, yellow-pigmented bacterium, designated strain XH208T, was isolated from a deep subseafloor sediment sample collected from the South Pacific Gyre (41° 58′ S 163° 11′ W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XH208T belonged to the genus
Luteococcus
and showed the highest 16S rRNA gene sequence similarities with
Luteococcus peritonei
CCUG 38120T (96.9 %),
Luteococcus japonicus
DSM 10546T (95.4 %) and
Luteococcus sanguinis
CCUG 33897T (95.2 %). The DNA G+C content of strain XH208T was 66.9 mol%. The cell wall of strain XH208T possessed a type A3γ peptidoglycan (ll-diaminopimelic acid–glycine), and ribose, glucose and galactose as the major whole-cell sugars. The major fatty acids were C17 : 1ω8c, C17 : 1ω6c, and C16 : 1ω6c and/or C16 : 1ω7c (summed feature 3). The major respiratory quinone was menaquinone MK-9(H4). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol. On the basis of data from the polyphasic analysis, strain XH208T is considered to represent a novel species in the genus
Luteococcus
, for which the name Luteococcus
sediminum sp. nov. is proposed. The type strain is XH208T ( = DSM 27277T = JCM 19259T).
Collapse
Affiliation(s)
- Xiaoyang Fan
- College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
| | - Zenghu Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
| | - Zhao Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
| |
Collapse
|
35
|
Karl JP, Fu X, Dolnikowski GG, Saltzman E, Booth SL. Quantification of phylloquinone and menaquinones in feces, serum, and food by high-performance liquid chromatography-mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 963:128-33. [PMID: 24956079 DOI: 10.1016/j.jchromb.2014.05.056] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 05/21/2014] [Accepted: 05/28/2014] [Indexed: 10/25/2022]
Abstract
Vitamin K, comprising phylloquinone (PK) and menaquinones (MKn), is a family of vitamers found in multiple biological and environmental matrices. Advancing emerging evidence for novel and distinct physiologic roles of these vitamers in human health and disease necessitates sensitive and selective methods for quantifying PK and MKn in these matrices. We developed a novel method employing high-performance liquid chromatography-mass spectrometry with atmospheric pressure chemical ionization (LC-APCI-MS) for simultaneous quantification of 11 vitamin K vitamers that can be applied in feces, serum and food. Minimal detectable concentrations of vitamin K vitamers ranged from 1 pmol/g to 30 pmol/g. Limits of quantification ranged from 5 pmol/g to 90 pmol/g. Inter-assay and intra-assay variations were <17% and <8%, respectively, in food, and <12% and <8%, respectively, in feces. Recovery exceeded 80% for all vitamers in both food and feces. The method successfully quantified PK and MKn concentrations in rat chow, feces and serum. In summary, this LC-APCI-MS method provides a sensitive and selective tool for quantifying vitamin K vitamers in feces, serum and food. This method can be applied in human and animal studies examining the role of vitamin K vitamers derived from the diet and gut bacteria synthesis in health and disease.
Collapse
Affiliation(s)
- J Philip Karl
- Vitamin K Laboratory, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, 711 Washington St, Boston, MA 02111, United States; Energy Metabolism Laboratory, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, 711 Washington St, Boston, MA 02111, United States
| | - Xueyan Fu
- Vitamin K Laboratory, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, 711 Washington St, Boston, MA 02111, United States
| | - Gregory G Dolnikowski
- Mass Spectrometry Unit, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, 711 Washington St, Boston, MA 02111, United States
| | - Edward Saltzman
- Energy Metabolism Laboratory, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, 711 Washington St, Boston, MA 02111, United States
| | - Sarah L Booth
- Vitamin K Laboratory, Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, 711 Washington St, Boston, MA 02111, United States.
| |
Collapse
|
36
|
Hyun DW, Shin NR, Kim MS, Oh SJ, Kim PS, Whon TW, Bae JW. Endozoicomonas atrinae sp. nov., isolated from the intestine of a comb pen shell Atrina pectinata. Int J Syst Evol Microbiol 2014; 64:2312-2318. [PMID: 24733175 DOI: 10.1099/ijs.0.060780-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium, designated strain WP70(T), was isolated from the gut of a comb pen shell (Atrina pectinata) collected from the southern sea of Yeosu in Korea. The isolate was Gram-stain-negative, aerobic, non-motile and rod-shaped. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain WP70(T) belonged to the genus Endozoicomonas. The highest level of sequence similarity (98.4%) was shared with Endozoicomonas elysicola MKT110(T). Optimal growth occurred in 2% (w/v) NaCl at 30 °C and at pH 7. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The main respiratory quinone was Q-9. The polar lipids comprised phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, three unidentified phospholipids, an unidentified aminolipid, an unidentified aminophospholipid and an unidentified lipid. The genomic DNA G+C content was 50.5 mol% and DNA-DNA hybridization values indicated <11% genomic relatedness to the closest species. Physiological, biochemical, chemotaxonomic and genotypic analyses indicated that strain WP70(T) represents a novel species of the genus Endozoicomonas, for which the name Endozoicomonas atrinae sp. nov. is proposed. The type strain is WP70(T) ( = KACC 17474(T) = JCM 19190(T)).
Collapse
Affiliation(s)
- Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Min-Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Sei Joon Oh
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Pil Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Tae Woong Whon
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| |
Collapse
|
37
|
Lorantfy B, Renkecz T, Koch C, Horvai G, Lendl B, Herwig C. Identification of lipophilic bioproduct portfolio from bioreactor samples of extreme halophilic archaea with HPLC-MS/MS. Anal Bioanal Chem 2014; 406:2421-32. [PMID: 24510212 DOI: 10.1007/s00216-014-7626-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 01/10/2014] [Accepted: 01/13/2014] [Indexed: 10/25/2022]
Abstract
Extreme halophilic archaea are a yet unexploited source of natural carotenoids. At elevated salinities, however, material corrosivity issues occur and the performance of analytical methods is strongly affected. The goal of this study was to develop a method for identification and downstream processing of potentially valuable bioproducts produced by archaea. To circumvent extreme salinities during analysis, a direct sample preparation method was established to selectively extract both the polar and the nonpolar lipid contents of extreme halophiles with hexane, acetone and the mixture of MeOH/MTBE/water, respectively. Halogenated solvents, as used in conventional extraction methods, were omitted because of environmental considerations and potential process scale-up. The HPLC-MS/MS method using atmospheric pressure chemical ionization was developed and tuned with three commercially available C40 carotenoid standards, covering the wide polarity range of natural carotenoids, containing different number of OH-groups. The chromatographic separation was achieved on a C30 RP-HPLC column with a MeOH/MTBE/water gradient. Polar lipids, the geometric isomers of the C50 carotenoid bacterioruberin, and vitamin MK-8 were the most valuable products found in bioreactor samples. In contrast to literature on shake flask cultivations, no anhydrous analogues of bacterioruberin, as by-products of the carotenoid biosynthesis, were detected in bioreactor samples. This study demonstrates the importance of sample preparation and the applicability of HPLC-MS/MS methods on real samples from extreme halophilic strains. Furthermore, from a biotechnological point-of-view, this study would like to reveal the relevance of using controlled and defined bioreactor cultivations instead of shake flask cultures in the early stage of potential bioproduct profiling.
Collapse
Affiliation(s)
- Bettina Lorantfy
- Research Division Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1A 166/4, 1060, Vienna, Austria
| | | | | | | | | | | |
Collapse
|
38
|
A rapid method for the extraction and analysis of carotenoids and other hydrophobic substances suitable for systems biology studies with photosynthetic bacteria. Metabolites 2013; 3:912-30. [PMID: 24958257 PMCID: PMC3937835 DOI: 10.3390/metabo3040912] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 09/26/2013] [Accepted: 09/27/2013] [Indexed: 11/17/2022] Open
Abstract
A simple, rapid, and inexpensive extraction method for carotenoids and other non-polar compounds present in phototrophic bacteria has been developed. The method, which has been extensively tested on the phototrophic purple non-sulphur bacterium Rhodospirillum rubrum, is suitable for extracting large numbers of samples, which is common in systems biology studies, and yields material suitable for subsequent analysis using HPLC and mass spectroscopy. The procedure is particularly suitable for carotenoids and other terpenoids, including quinones, bacteriochlorophyll a and bacteriopheophytin a, and is also useful for the analysis of polar phospholipids. The extraction procedure requires only a single step extraction with a hexane/methanol/water mixture, followed by HPLC using a Spherisorb C18 column, with a mobile phase consisting of acetone-water and a non-linear gradient of 50%-100% acetone. The method was employed for examining the carotenoid composition observed during microaerophilic growth of R. rubrum strains, and was able to determine 18 carotenoids, 4 isoprenoid-quinones, bacteriochlorophyll a and bacteriopheophytin a as well as four different phosphatidylglycerol species of different acyl chain compositions. The analytical procedure was used to examine the dynamics of carotenoid biosynthesis in the major and minor pathways operating simultaneously in a carotenoid biosynthesis mutant of R. rubrum.
Collapse
|
39
|
Kim SH, Liu KH, Lee SY, Hong SJ, Cho BK, Lee H, Lee CG, Choi HK. Effects of light intensity and nitrogen starvation on glycerolipid, glycerophospholipid, and carotenoid composition in Dunaliella tertiolecta culture. PLoS One 2013; 8:e72415. [PMID: 24039760 PMCID: PMC3764108 DOI: 10.1371/journal.pone.0072415] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 07/09/2013] [Indexed: 11/18/2022] Open
Abstract
Time-course variation of lipid and carotenoid production under high light (300 μE/m2s) and nitrogen starvation conditions was determined in a Dunaliella tertiolecta strain. Nanoelectrospray (nanoESI) chip based direct infusion was used for lipid analysis and ultra-performance liquid chromatography (UPLC) coupled with a photodiode array (PDA) or atmospheric chemical ionization mass spectrometry (APCI-MS) was used for carotenoid analysis. A total of 29 lipids and 7 carotenoids were detected. Alterations to diacylglyceryltrimethylhomoserine (DGTS) and digalactosyldiacylglycerol (DGDG) species were significant observations under stress conditions. Their role in relation to the regulation of photosynthesis under stress condition is discussed in this study. The total carotenoid content was decreased under stress conditions, while ã-carotene was increased under nitrate-deficient cultivation. The highest productivity of carotenoid was attained under high light and nitrate sufficiency (HLNS) condition, which result from the highest level of biomass under HLNS. When stress was induced at stationary phase, the substantial changes to the lipid composition occurred, and the higher carotenoid content and productivity were exhibited. This is the first report to investigate the variation of lipids, including glycerolipid, glycerophospholipid, and carotenoid in D. tertiolecta in response to stress conditions using lipidomics tools.
Collapse
Affiliation(s)
- So-Hyun Kim
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Kwang-Hyeon Liu
- College of Pharmacy, Kyungpook National University, Daegu, Republic of Korea
| | - Seok-Young Lee
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Seong-Joo Hong
- Institute of Industrial Biotechnology, Department of Biological Engineering, Inha University, Incheon, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - Hookeun Lee
- College of Pharmacy, Gachon University, Incheon, Republic of Korea
| | - Choul-Gyun Lee
- Institute of Industrial Biotechnology, Department of Biological Engineering, Inha University, Incheon, Republic of Korea
| | - Hyung-Kyoon Choi
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
- * E-mail:
| |
Collapse
|