LC–MS method for screening unknown microbial carotenoids and isoprenoid quinones

Bacterial Carotenoids: Extraction, Characterization, and Applications

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.

Isolation, Characterization, and Antibiofilm Activity of Pigments Synthesized by Rhodococcus sp. SC1

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.

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

A novel Gram-staining positive, aerobic, rod-shaped, non-motile and yellow-pigmented actinobacterium, designated strain WY83^T, was isolated from a marine sediment of Indian Ocean. Strain WY83^T 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 C_19:1 ω9c/C19:1 ω11c, anteiso-C_15:0, C_17:0 3OH, and iso-C_16:0. 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 WY83^T formed an evolutionary lineage with Chryseoglobus frigidaquae JCM 14730^T, Chryseoglobus indicus CTD02-10-2^T, Yonghaparkia alkaliphila JCM 15138^T, Microcella alkaliphila DSM 18851^T and Microcella putealis DSM 19627^T within the radiation enclosing members of the family Microbacteriaceae. All pairwise percentage of conserved proteins between strain WY83^T 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 WY83^T, Y. alkaliphila JCM 15138^T, C. frigidaquae JCM 14730^T, M. alkaliphila DSM 18851^T and M. putealis DSM 19627^T should belong to different species of the same genus. Strain WY83^T represents a novel species of the genus Microcella, for which the name Microcella flavibacter sp. nov. is proposed. The type strain is WY83^T (= KCTC 39637^T = MCCC 1A07099^T). 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.

Brevibacterium limosum sp. nov., Brevibacterium pigmenatum sp. nov., and Brevibacterium atlanticum sp. nov., three novel dye decolorizing actinobacteria isolated from ocean sediments

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 o2^T, YB235^T, and WO024^T 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 YB235^T, WO024^T, and o2^T 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 o2^T, YB235^T and WO024^T clearly represent three novel taxa within the genus Brevibacterium, for which the names Brevibacterium limosum sp. nov. (type strain o2^T = JCM 33844^T = MCCC 1A09961^T), Brevibacterium pigmenatum sp. nov. (type strain YB235^T = JCM 33843^T = MCCC 1A09842^T) and Brevibacterium atlanticum sp. nov. (type strain WO024^T = JCM 33846^T = MCCC 1A16743^T) are proposed.

Genomics- and Metabolomics-Based Investigation of the Deep-Sea Sediment-Derived Yeast, Rhodotorula mucilaginosa 50-3-19/20B

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.

Chryseoglobus indicus sp. nov., isolated from deep sea water

A novel Gram-stain-positive, motile, aerobic, non-spore-forming and slender rod-shaped actinobacterium, designated strain CTD02-10-2^T, was isolated from deep sea water of the Indian Ocean. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CTD02-10-2^T was grouped into a separated branch with Chryseoglobus frigidaquae JCM 14730^T (98.4 % nucleotide sequence identity). The respiratory quinones were menaquinones with 11, 12, 13 and 14 isoprene units and anteiso-C_15 : 0, iso-C_16 : 0, anteiso-C_15 : 1 A and anteiso-C_17 : 0 were the major fatty acids. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and three unknown glycolipids. The genome of strain CTD02-10-2^T 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 CTD02-10-2^T and C. frigidaquae JCM 14730^T 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 CTD02-10-2^T was classified as a novel species of the genus Chryseoglobus, for which the name Chryseoglobus indicus sp. nov. is proposed. The type strain is CTD02-10-2^T (=JCM 33842^T=MCCC 1A16619^T).

Brevibacterium profundi sp. nov., isolated from deep-sea sediment of the Western Pacific Ocean

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).

Paraburkholderia solitsugae sp. nov. and Paraburkholderia elongata sp. nov., phenolic acid-degrading bacteria isolated from forest soil and emended description of Paraburkholderia madseniana

Two bacterial strains, 1N^T and 5N^T, were isolated from hemlock forest soil using a soluble organic matter enrichment. Cells of 1N^T (0.65×1.85 µm) and 5N^T (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 5N^T elongate (0.57×~7 µm) and form especially long filaments. Optimum growth of 1N^T and 5N^T occurred at 25-30 °C, pH 6.5-7.0 and <0.5% salinity. Results of comparative chemotaxonomic, genomic and phylogenetic analyses revealed that 1N^T and 5N^T were distinct from one another and their closest related type strains: Paraburkholderia madseniana RP11^T, Paraburkholderia aspalathi LMG 27731^T and Paraburkholderia caffeinilytica CF1^T. The genomes of 1N^T and 5N^T 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 1N^T and 5N^T from each other and their closest relatives. The only ubiquinone present in strains 1N^T and 5N^T was Q-8. The major cellular fatty acids were C_{16 : 0}, 3OH-C_{16 : 0}, C_{17 : 0} cyclo, C_{19 : 0} cyclo ω8c and summed features 2 (3OH-C_{14 : 0} / C_{16 : 1} iso I), 3 (C_{16 : 1} ω6c/ω7c) and 8 (C_{18 : 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 1N^T and 5N^T represent novel species from the genus Paraburkholderia for which the names Paraburkholderia solitsugae sp. nov. (type strain 1N^T=DSM 110721^T=LMG 31704^T) and Paraburkholderia elongata sp. nov. (type strain 5N^T=DSM 110722^T=LMG 31705^T) are proposed.

Saccharopolyspora coralli sp. nov. a novel actinobacterium isolated from the stony coral Porites

A novel Gram-stain-positive, aerobic, non-motile actinobacterium, designated strain E2A^T, was isolated from a coral sample and examined using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain E2A^T formed a distinct phyletic lineage in the genus Saccharopolyspora and was closely related to S. cavernae CCTCC AA 2012022^T (96.4 %) and S. lacisalsi CCTCC AA 2010012^T (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-C_15 : 0, iso-C_16 : 0 and C_17 : 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 E2A^T represents a novel species within the genus Saccharopolyspora, for which the name Saccharopolyspora coralli sp. nov. is proposed. The type strain is E2A^T=(JCM 31844^T=MCCC 1A17150^T).

Exploring the Lipidome: Current Lipid Extraction Techniques for Mass Spectrometry Analysis

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.

Paraburkholderia madseniana sp. nov., a phenolic acid-degrading bacterium isolated from acidic forest soil

RP11^T was isolated from forest soil following enrichment with 4-hydroxybenzoic acid. Cells of RP11^T 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 27731^T, Paraburkholderia fungorum LMG 16225^T and Paraburkholderia caffeinilytica CF1^T. Strain RP11^T 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 RP11^T from its closest relatives, including growth on phthalic acid. Strain RP11^T 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 RP11^T was Q-8, and the major cellular fatty acids were C_16 : 0, 3OH-C_16 : 0, C_17 : 0 cyclo, C_19 : 0 cyclo ω8c, and summed feature 8 (C_18 : 1 ω7c/ω6c). On the basis of this polyphasic approach, it was determined that strain RP11^T represents a novel species from the genus Paraburkholderia for which the name Paraburkholderia madseniana sp. nov. is proposed. The type strain is RP11^T (=DSM 110123^T=LMG 31517^T).

Pseudomonas rhizoryzae sp. nov., isolated from rice

Two yellow-pigmented, Gram-stain-negative and rod-shaped bacterial strains, designated as RY24^T and ZYY160, were isolated from rice. Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strains RY24^T 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 1.3392^T and Pseudomonas psychrotolerans DSM 15758^T (sharing 99.31 and 94.34 %, respectively). The major fatty acids of two strains were identified as summed feature 8 (C_18:1ω7c and/or C_18:1ω6c), C_16;0 and summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), 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 RY24^T 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 RY24^T 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 RY24^T (JCM 33201^T=ACCC 61555^T), for which the name Pseudomonas rhizoryzae sp. nov. is proposed.

The Methoxylated, Highly Conjugated C40 Carotenoids, Spirilloxanthin and Anhydrorhodovibrin, Can Be Separated Using High Performance Liquid Chromatography with Safe and Environmentally Friendly Solvents

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.

Characterization of MK₈(H₂) from Rhodococcus sp. B7740 and Its Potential Antiglycation Capacity Measurements

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.

Identification of Carotenoids and Isoprenoid Quinones from Asaia lannensis and Asaia bogorensis

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.

Identification of microbial carotenoids and isoprenoid quinones from Rhodococcus sp. B7740 and its stability in the presence of iron in model gastric conditions

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.

Important roles for membrane lipids in haloarchaeal bioenergetics

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.

Proteus cibarius sp. nov., a swarming bacterium from Jeotgal, a traditional Korean fermented seafood, and emended description of the genus Proteus

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.

Sediminivirga luteola gen. nov., sp. nov., a member of the family Brevibacteriaceae, isolated from marine sediment

A Gram-stain-positive actinobacterial strain, designated F23^T, was isolated from marine sediment collected from the western Pacific. Strain F23^T 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 F23^T 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-C_15 : 0 and anteiso-C_17 : 0 as the major fatty acids. The DNA G+C content of strain F23^T was 69.0 mol%. On the basis of phylogenetic analysis, phenotypic and chemotaxonomic characteristics and 16S rRNA gene signature nucleotide patterns, strain F23^T 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 F23^T ( = JCM 19771^T = CGMCC 1.12785^T = MCCC 1A09945^T).

Carotenoid Production by Halophilic Archaea Under Different Culture Conditions

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.

Respiratory quinones in Archaea: phylogenetic distribution and application as biomarkers in the marine environment

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.

Simplicispira piscis sp. nov., isolated from the gut of a Korean rockfish, Sebastes schlegelii

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).

Actibacter haliotis sp. nov., isolated from the gut of an abalone, Haliotis discus hannai, and emended description of the genus Actibacter

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).

Citrimicrobium luteum gen. nov., sp. nov., aerobic anoxygenic phototrophic bacterium isolated from the gut of a sea cucumber Stichopus japonicus

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)).

Luteococcus sediminum sp. nov., isolated from deep subseafloor sediment of the South Pacific Gyre

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).

Quantification of phylloquinone and menaquinones in feces, serum, and food by high-performance liquid chromatography-mass spectrometry

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.

Endozoicomonas atrinae sp. nov., isolated from the intestine of a comb pen shell Atrina pectinata

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)).

Identification of lipophilic bioproduct portfolio from bioreactor samples of extreme halophilic archaea with HPLC-MS/MS

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.

A rapid method for the extraction and analysis of carotenoids and other hydrophobic substances suitable for systems biology studies with photosynthetic bacteria

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.

Effects of light intensity and nitrogen starvation on glycerolipid, glycerophospholipid, and carotenoid composition in Dunaliella tertiolecta culture

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.