Virgibacillus tibetensis sp. nov., isolated from salt lake on the Tibetan plateau of China.

One bacterial strain, designated as C22-A2T, was isolated from Lake LungmuCo in Tibet. Cells of strain C22-A2T were long rod-shaped, Gram-stain-negative, non-spore-forming, with positive catalase and oxidase activity. Optimal growth occurred at 20-25 °C, pH 8.0 and with 3.0-7.0% (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene and whole genome sequences revealed that strain C22-A2T belonged to the genus Virgibacillus, showing the highest 16S rRNA gene similarity to Virgibacillus halodenitrificans DSM 10037T (97.6%). The average nucleotide identity values between strain C22-A2T and the type strains of related species in the genus Virgibacillus were less than 74.4% and the digital DNA-DNA hybridization values were less than 20.2%, both below the species delineation thresholds of 95 and 70% respectively. The genome analysis revealed that strain C22-A2T harboured genes responsible for osmotic and oxidative stress, enabling it to adapt to its surrounding environment. In terms of biochemical and physiological characteristics, strain C22-A2T shared similar characteristics with the genus Virgibacillus, including the predominant cellular fatty acid anteiso-C15 : 0, the major respiratory quinone MK-7, as well as the polar lipids phosphatidylglycerol and diphosphatidylglycerol. Based on the comprehensive analysis of phylogenetic, phylogenomic, morphological, physiological and biochemical characteristics, strain C22-A2T is proposed to represent a novel species of the genus Virgibacillus, named as Virgibacillus tibetensis sp. nov. (=CGMCC 1.19202T=KCTC 43426T).

Paralabilibaculum antarcticum gen. nov., sp. nov., an anaerobic marine bacterium of the family Marinifilaceae isolated from Antarctica sea ice.

A novel bacterial strain, designated DW002T, was isolated from the sea ice of Cape Evans, McMurdo Sound, Antarctica. Cells of the strain were Gram-negative, obligate anaerobic, motile, non-flagellated, and short rod-shaped. The strain DW002T grew at 4-32 â„ƒ (optimum at 22-28 â„ƒ) and thrived best at pH 7.0, NaCl concentration of 2.5% (w/v). The predominant isoprenoid quinone of strain DW002T was menaquinone-7 (MK-7). The major fatty acids (> 10%) of DW002T were iso-C15:0, anteiso-C15:0 and iso-C17:1ω9c. The predominant polar lipids of strain DW002T contained two phosphatidylethanolamines, one unidentified glycolipid, one unidentified aminolipid and four unidentified lipids. The DNA G + C content of the strain DW002T was 34.8%. Strain DW002T encoded 237 carbohydrate-active enzymes. The strain DW002T had genes associated with dissimilatory nitrate reduction and assimilatory sulfate reduction metabolic pathways. Based on distinct physiological, chemotaxonomic, genome analysis and phylogenetic differences compared to other members of the phylogenetically related genera in the family Marinifilaceae, strain DW002T is proposed to represent a novel genus within the family. Therefore, the name Paralabilibaculum antarcticum gen. nov., sp. nov. is proposed. The type strain is DW002T (=KCTC 25274T=MCCC 1K06067T).

LC-HRMS analysis of phospholipids bearing oxylipins.

BACKGROUND: Several oxylipins including hydroxy- and epoxy-polyunsaturated fatty acids act as lipid mediators. In biological samples they can be present as non-esterified form, but the major part occurs esterified in phospholipids (PL) or other lipids. Esterified oxylipins are quantified indirectly after alkaline hydrolysis as non-esterified oxylipins. However, in this indirect analysis the information in which lipid class oxylipins are bound is lost. In this work, an untargeted liquid chromatography high-resolution mass spectrometry (LC-HRMS) method for the direct analysis of PL bearing oxylipins was developed. RESULTS: Optimized reversed-phase LC separation achieved a sufficient separation of isobaric and isomeric PL from different lipid classes bearing oxylipin positional isomers. Individual PL species bearing oxylipins were identified based on retention time, precursor ion and characteristic product ions. The bound oxylipin could be characterized based on product ions resulting from the α-cleavage occurring at the hydroxy/epoxy group. PL sn-1/sn-2 isomers were identified based on the neutral loss of the fatty acyl in the sn-2 position. A total of 422 individual oxPL species from 7 different lipid classes i.e., PI, PS, PC, PE, PC-P, PC-O, and PE-P were detected in human serum and cells. This method enabled to determine in which PL class supplemented oxylipins are incorporated in HEK293 cells: 20:4;15OH, 20:4;14Ep, and 20:5;14Ep were mostly bound to PI. 20:4;8Ep and 20:5;8Ep were esterified to PC and PE while other oxylipins were mainly found in PC. SIGNIFICANCE: The developed LC-HRMS method enables the comprehensive detection as well as the semi-quantification of isobaric and isomeric PL species bearing oxylipins. With this method, we show that the position of the oxidation has a great impact and directs the incorporation of oxylipins into the different PL classes in human cells.

Paracraurococcus lichenis sp. nov., isolated from lichen in Thailand.

A novel bacterium, designated as strain LOR1-02T and isolated from a lichen sample collected from Kham Riang Subdistrict, Kantharawichai District, Maha Sarakham Province, Thailand, underwent thorough investigation utilizing a polyphasic taxonomic approach. Strain LOR1-02T demonstrated growth within a temperature range of 20-42 °C (optimal at 30 °C), pH range of 5.0-7.5 (optimal at pH 7.0), and tolerance to 4.0% (w/v) NaCl. Phylogenetic analysis revealed its close relation to Paracraurococcus ruber JCM 9931T, with a 16S rRNA gene sequence similarity of 97.16%, placing it within the genus Paracraurococcus. The approximate genome size of strain LOR1-02T was determined to be 8.6 Mb, with a G + C content of 70.9 mol%. Additionally, ANIb, ANIm, and AAI values between the whole genomes of strain LOR1-02T and type strains were calculated as 82.6-83.4%, 86.1-86.8%, and 81.4-82.2%, respectively, while the dDDH value was determined to be 26.3-28.5% (C.I. 24.0-31.0%). The predominant fatty acids detected were C18:1ω7c and/or C18:1ω6c, C16:0, and C18:12OH. The major ubiquinone identified was Q-10, and the polar lipids included phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, along with unidentified phosphoaminolipid, lipids, and an amino lipid. Based on comprehensive phenotypic, chemotaxonomic, and genotypic characterization, it is concluded that strain LOR1-02T represents a novel species within the genus Paracraurococcus, for which the name Paracraurococcus lichenis sp. nov. is proposed. The type strain designation is LOR1-02T (= JCM 33121T = NBRC 112776T = TISTR 2503T).

A novel strategy of bloom forming cyanobacteria Microcystis sp. in response to phosphorus deficiency: Using non-phosphorus lipids substitute phospholipids.

Despite significant reductions in phosphorus (P) loads, lakes still experience cyanobacterial blooms. Little is known regarding cellular P regulation in response to P deficiency in widely distributed bloom causing species such as Microcystis. In this study, we investigated changes in P containing and non-P lipids contents and their ratios concomitantly with the determinations of expression levels of genes encoding these lipids in cultural and field Microcystis samples. In the culture, the content of phosphatidylglycerol (PG) decreased from 2.1 µg g-1 in P replete control to 1.2 µg g-1 in P-deficient treatment, while non-P lipids, like sulfoquinovosyldiacylglycerol (SQDG) and monogalactosyldiacylglycerol (MGDG), increased dramatically from 13.6 µg g-1 to 142.3 µg g-1, and from 0.9 µg g-1 to 16.74 µg g-1, respectively. The expression of the MGDG synthesis gene, mgdE, also increased under low P conditions. Significant positive relationships between soluble reactive phosphorus (SRP) and ratios of P-containing lipids (PG) to non-P lipids, including SQDG, MGDG and digalactosyldiacylglycerol (DGDG) (P < 0.05) were observed in the field investigations. Both cultural and field data indicated that Microcystis sp. might increase non-P lipids proportion to lower P demand when suffering from P deficiency. Furthermore, despite lipid remodeling, photosynthetic activity remained stable, as indicated by comparable chlorophyll fluorescence and Fv/Fm ratios among cultural treatments. These findings suggested that Microcystis sp. may dominate in P-limited environments by substituting glycolipids and sulfolipids for phospholipids to reduce P demand without compromising the photosynthetic activity. This effective strategy in response to P deficiency meant a stricter P reduction threshold is needed in terms of Microcystis bloom control.

Polaribacter ponticola sp. nov., isolated from seawater, reclassification of Polaribacter undariae as a later heterotypic synonym of Polaribacter sejongensis, and emended description of Polaribacter sejongensis Kim et al. 2013.

A Gram-stain-negative, yellow-pigmented, and strictly aerobic bacterium, designated as strain MSW5T, was isolated from seawater of the Yellow Sea in South Korea. The cells were non-motile rods exhibiting oxidase- and catalase-positive activities. Growth was observed at 15-25 °C (optimum, 25 °C) and pH 5.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 1.0-5.0% (w/v) NaCl (optimum, 2.0%). Menaquinone-6 was the sole respiratory quinone, and iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C15 : 0 3-OH, and C15 : 1 ω6c were the major cellular fatty acids. Major polar lipids included phosphatidylethanolamine, two unidentified aminolipids, and three unidentified lipids. Phylogenetic analyses based on 16S rRNA gene sequences and 92 concatenated core protein sequences revealed that strain MSW5T formed a distinct lineage within the genus Polaribacter. The genome of strain MSW5T was 3582 kb in size with a 29.1 mol% G+C content. Strain MSW5T exhibited the highest similarity to Polaribacter atrinae WP25T, with a 97.9% 16S rRNA gene sequence similarity. However, the average nucleotide identity and digital DNA-DNA hybridization values were 79.4 and 23.3%, respectively, indicating that strain MSW5T represents a novel species. Based on its phenotypic, chemotaxonomic, and phylogenetic characteristics, strain MSW5T is proposed to represent a novel species, with the name Polaribacter ponticola sp. nov. The type strain is MSW5T (=KACC 22340T=NBRC 116025T). In addition, whole genome sequence comparisons and phenotypic features suggested that Polaribacter sejongensis and Polaribacter undariae belong to the same species, with P. undariae proposed as a later heterotypic synonym of P. sejongensis. An emended description of Polaribacter sejongensis is also proposed.

Hyphobacterium marinum sp. nov. and Hyphobacterium lacteum sp. nov., isolated from marine sediment.

Two bacterial strains, Y60-23T and HN-65T, were isolated from marine sediment samples collected from Xiaoshi Island, Weihai, and Dongzhai Harbour, Haikou, PR China, respectively. Based on the 16S rRNA gene sequences, strain Y60-23T exhibited 96.0% similarity to its most related type strain Hyphobacterium vulgare KCTC 52487T, while strain HN-65T exhibited 97.3% similarity to its most related type strain Hyphobacterium indicum 2ED5T. The 16S rRNA gene sequence similarity between the two strains was 95.8%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains Y60-23T and HN-65T belonged to the genus Hyphobacterium. Cells of strains Y60-23T and HN-65T were rod-shaped, Gram-stain-negative, aerobic, non-motile, prosthecate and multiplied by binary fission. The major cellular fatty acids (>10.0%) of strain Y60-23T were C18 : 1 ω7c and C17 : 0, while those of strain HN-65T were iso-C17 : 1 ω9c, iso-C17 : 0 and C18 : 1 ω7c. The major respiratory quinone in both strains was ubiquinone-10 (Q-10) and the major polar lipids were monoglycosyl diglyceride, sulfoquinovosyl diacylglycerol and glucuronopyranosyl diglyceride. The genomic DNA G+C contents of strains Y60-23T and HN-65T were 63.9 and 60.7 mol%, respectively. The average nucleotide identity value between the two strains was 72.1% and the DNA-DNA hybridization value was 18.4%, clearly distinguishing them from each other. According to the results of the phenotypic, chemotaxonomic, phylogenetic and genomic analyses, the two strains represented two novel species within the genus Hyphobacterium, for which the names Hyphobacterium marinum sp. nov. and Hyphobacterium lacteum sp. nov. were proposed with the type strains Y60-23T (=MCCC 1H01433T=KCTC 8172T) and HN-65T (=MCCC 1H01434T=KCTC 8169T), respectively.

Aequorivita flava sp. nov., isolated from deep-sea sediments.

Three Gram-stain-negative, aerobic, non-motile, chemoheterotrophic, short-rod-shaped bacteria, designated CDY1-MB1T, CDY2-MB3, and BDY3-MB2, were isolated from three marine sediment samples collected in the eastern Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains were related to the genus Aequorivita and close to the type strain of Aequorivita vitellina F4716T (with similarities of 98.0-98.1%). Strain CDY1-MB1T can grow at 15-37 °C (optimum 30 °C) and in media with pH 6-9 (optimum, pH 7), and tolerate up to 10% (w/v) NaCl. The predominant cellular fatty acids of strain CDY1-MB1T were iso-C15 : 0 (20.7%) and iso-C17 : 0 3-OH (12.8%); the sole respiratory quinone was menaquinone 6; the major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and two unidentified polar lipids. The digital DNA-DNA hybridization/average nucleotide identity values between strains CDY1-MB1T, CDY2-MB3, and BDY3-MB2 and A. vitellina F4716T were 24.7%/81.6-81.7%, thereby indicating that strain CDY1-MB1T should represent a novel species of the genus Aequorivita. The genomic DNA G+C contents were 37.6 % in all three strains. Genomic analysis showed the presence of genes related to nitrogen and sulphur cycling, as well as metal reduction. The genetic traits of these strains indicate their possible roles in nutrient cycling and detoxification processes, potentially shaping the deep-sea ecosystem's health and resilience. Based upon the consensus of phenotypic and genotypic analyses, strain CDY1-MB1T should be classified as a novel species of the genus Aequorivita, for which the name Aequorivita flava sp. nov. is proposed. The type strain is CDY1-MB1T (=MCCC 1A16935T=KCTC 102223T).

Microbial community characteristics and their influencing factors in Caragana korshinskii sand-fixing forests of different restoration years in the Mu Us Desert, China.

Soil microorganisms play a crucial role as a link between vegetation and soil nutrient cycling. However, it is unclear how vegetation and soil influence microbial community during the ecological restoration process of the Mu Us Desert. Using phospholipid fatty acid (PLFA) markers and integrating shrub, herbaceous plants, and soil factors, we explored the characteristics and regulations of soil microbial community changes. In this study, we used and took the soil after 10, 30, 50, and 70 years of Caragana korshinskii sand-fixing forest restoration, with moving dunes as a control (0 year). The results showed that the ecological restoration effect index increased significantly with the increase of recovery years. The total PLFA contents in 0, 10, 30, 50, and 70 years were 47.75, 55.89, 63.53, 67.23, and 82.29 nmol·g-1, respectively. With the increases of ecological restoration index, the biomass of fungi and bacteria, as well as the ratio of Gram-positive to Gram-negative bacteria, all showed significant increase, while the biomass of Gram-positive and Gram-negative bacterial communities, and the ratio of fungi to bacteria, demonstrated significant decrease. Shrub, herbaceous plants, and soil factors could explain 72.4% of the vari-ation of soil microbial community composition, with higher contribution of soil factors than vegetation factors. The total content of phospholipid fatty acids of soil microbial community in Mu Us Desert increased with the increases of restoration years. Soil water content, pH, total nitrogen, and soil organic carbon were the main driving factors affecting the characteristics of soil microbial community. With the increases of restoration years of C. korshinskii sand-fixation forests in the Mu Us Desert, there were significant changes in the structure of soil microbial communities, which were primarily driven by soil factors.

Atacama desert is a source of new Micromonospora strains: description of Micromonospora sicca sp. nov.

Several strains were isolated from subsurface soil of the Atacama Desert and were previously assigned to the Micromonospora genus. A polyphasic study was designed to determine the taxonomic affiliation of isolates 4G51T, 4G53, and 4G57. All the strains showed chemotaxonomic properties in line with their classification in the genus Micromonospora, including meso-diaminopimelic acid in the cell wall peptidoglycan, MK-9(H4) as major respiratory quinone, iso-C15:0 and iso-C16:0 as major fatty acids and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as major polar lipids. The 16S rRNA gene sequences of strains 4G51T, 4G53, and 4G57 showed the highest similarity (97.9 %) with the type strain of Micromonospora costi CS1-12T, forming an independent branch in the phylogenetic gene tree. Their independent position was confirmed with genome phylogenies, being most closely related to the type strain of Micromonospora kangleipakensis. Digital DNA-DNA hybridization and average nucleotide identity analyses between the isolates and their closest phylogenomic neighbours confirmed that they should be assigned to a new species within the genus Micromonospora for which the name Micromonospora sicca sp. nov. (4G51T=PCM 3031T=LMG 30756T) is proposed.

Evaluation of simplified ester-linked fatty acid analysis (ELFA) for phospholipid fatty acid (PLFA) analysis of bacterial population.

Phospholipid fatty acid (PLFA) analysis is used for characterizing microbial communities based on their lipid profiles. This method avoids biases from PCR or culture, allowing data collection in a natural state. However, PLFA is labor-intensive due to lipid fractionation. Simplified ester-linked fatty acid analysis (ELFA), which skips lipid fractionation, offers an alternative. It utilizes base-catalyzed methylation to derivatize only lipids, not free fatty acids, and found glycolipid and neutral lipid fractions are scarcely present in most bacteria, allowing lipid fractionation to be skipped. ELFA method showed a high correlation to PLFA data (r = 0.99) and higher sensitivity than the PLFA method by 1.5-2.57-fold, mainly due to the higher recovery of lipids, which was 1.5-1.9 times higher than with PLFA. The theoretical limit of detection (LOD) and limit of quantification (LOQ) for the ELFA method indicated that 1.54-fold less sample was needed for analysis than with the PLFA method. Our analysis of three bacterial cultures and a simulated consortium revealed the effectiveness of the ELFA method by its simple procedure and enhanced sensitivity for detecting strain-specific markers, which were not detected in PLFA analysis. Overall, this method could be easily used for the population analysis of synthetic consortia.

Mycovorax composti gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from button mushroom compost.

Two Gram-stain-negative, aerobic, rod-shaped, orange-coloured bacterial strains, designated strain C216T and strain M2295, were isolated from mature mushroom compost from composting facilities in Victoria and South Australia, Australia, respectively. External structures such as flagella or pili were not observed on the cells under scanning electron microscopy. Optimal growth was found to occur at 45 °C, at pH 7.25 and in the absence of NaCl on Emerson's 350 YpSs medium. The genome sequence of strain C216T was 3 342 126 bp long with a G+C content of 40.5 mol%. Functional analysis of the genome of strain C216T revealed genes encoding chitinolytic and hemi-cellulolytic functions, with 166 predicted genes associated with carbohydrate metabolism (8.9% of the predicted genes). These functions are important for survival in the mushroom compost environment, which is rich in hemicelluloses. No antibiotic resistance genes were found in the genome sequence. The major fatty acids of strain C216T were iso-C15 : 0 (56.7%), iso-C17 : 0 3-OH (15.6%), C16 : 1 ω7c/iso-C15 : 0 2-OH (7.3%) and iso-C15 : 1 G (6.1%). The only respiratory quinone was MK-7. The major polar lipid of strain C216T was phosphatidylethanolamine, but three unidentified phospholipids, four unidentified aminophospholipids/aminolipids and one unidentified glycolipid were also detected. Phylogenetic analysis based on proteins encoded by the core genome (bac120, 120 conserved bacterial genes) showed that strain C216T forms a distinct lineage in the family Chitinophagaceae and that the closest identified relative is Niabella soli (69.69% ANI). These data demonstrate that strain C216T represents a novel genus and novel species within the family Chitinophagaceae, for which we propose the name Mycovorax composti. The type strain is C216T (=DSM 114558T=LMG 32998T).

Polar Localization Analysis of Anionic Phospholipids and Their Binding Proteins in Arabidopsis Pollen Tubes.

Pollen tubes are typical polarized growth cells whose elongation occurs only in tip regions and is highly dependent on precise and ordered exocytosis/endocytosis in the top regions of the tubes. Although anionic phospholipids have been proven to be involved in regulating vesicle trafficking and the proper localization and functions of proteins in pollen tubes, the underlying cellular and molecular mechanisms remain poorly understood. To further understand how anionic phospholipids are involved in vesicle trafficking and in the control of protein localization and functions, assay methods to analyze the polar localization of anionic phospholipids and their binding proteins, and identifying phospholipid-protein interactions, should be developed. Here, we describe detailed protocols for analyzing anionic phospholipid polar localization and colocalization with their binding proteins in Arabidopsis pollen tubes and examining phospholipid-protein interactions in vitro.

Rufibacter psychrotolerans sp. nov., a Cold-Tolerating Novel Species Isolated from Desert Soil.

Strain SYSU D00308T, a short-rod-shaped bacterium, was isolated from a sandy soil collected from the Gurbantunggut Desert, Xinjiang, PR China. Strain SYSU D00308T was Gram-stain-negative, aerobic, pink-pigmented, non-motile, catalase- and oxidase-positive. The strain grew at 4-37 ℃, pH 5.0-8.0 and 0-1.5% (w/v) NaCl. 16S rRNA gene sequencing analyses demonstrated that strain SYSU D00308T belonged to the genus Rufibacter and exhibited the highest sequence similarity (97.4%) to Rufibacter glacialis MDT1-10-3T. Summed features 3, 4, and iso-C15:0 were the major fatty acids, and menaquinone 7 (MK-7) was the sole respiratory menaquinone. The polar lipid profiles comprised phosphatidylethanolamine, an unidentified glycolipid, an unidentified phospholipid, two unidentified aminophospholipids, and two unidentified lipids. The genome size and DNA G + C content of strain SYSU D00308T were 5,176,683 bp and 54.8%, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between SYSU D00308T and members of the genus Rufibacter were 77.7-81.8% and 20.4-23.4% respectively, which were less than the corresponding thresholds (ANI: 95-96%; dDDH: 70%) for prokaryotic species definition. According to the genotypic, phenotypic and phylogenetic characteristics, strain SYSU D00308T represents a novel species of the genus Rufibacter. We propose the name, Rufibacter psychrotolerans sp. nov., with SYSU D00308T (= CGMCC 1.18621T = KCTC 82275T = MCCC 1K04970T) as the type strain.

Description of Aliirhizobium terrae sp. nov., A Plant Growth-Promoting Bacterium Isolated from a Maize-Rice Rotation Agriculture Field.

A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-CFT758T, isolated from a maize-rice rotation agriculture field in Taiwan. The cells are aerobic, Gram-stain-negative, rod-shaped, positive for catalase and oxidase, and grow at 20-30 °C (optimal 30 â„ƒ), at pH 6.0-8.0 (optimal 8.0), and with 0-4% (w/v) NaCl (optimum, 2-3%). Phylogenetic analysis based on 16S rRNA gene sequencing, the strain CC-CFT758T belongs to the genus "Aliirhizobium" of the family Rhizobiaceae. The closest known relatives of this strain are "Aliirhizobium wenxiniae" 166T (with 98.7% similarity), "Aliirhizobium cellulosilyticum" SEMIA 448T (with 97.9% similarity), and "Aliirhizobium smilacinae" PTYR-5T (with 97.0% similarity). The genome size was 5.9 Mbp, with a G + C content of 60.6%. Values of digital DNA-DNA hybridization between the strain and closely related species were 29.5% for "Ali. cellulosilyticum", and 23.9% for "Ali. wenxiniae" and "Ali. smilacinae". Strain CC-CFT758T exhibited the highest orthologous average nucleotide identity (OrthoANI) values with members of the genus "Aliirhizobium", ranging from 80.4 to 81.6% (n = 3). Chemotaxonomical analysis indicated that strain CC-CFT758T contained C16:0, C16:0 3OH, C19:0 cyclo ω8c, C14:0 3OH/iso-C16:1 I, and C18:2 ω6,9c/ante C18:0 as dominant fatty acids, and the major polyamines were putrescine and spermidine. The polar lipids comprised diphosphatidylglycerol, phosphatidylcholin, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, seven unidentified aminolipids, three unidentified phospholipids, and two unidentified polar lipids. Strain CC-CFT758T exhibited distinct phylogenetic, phenotypic, and chemotaxonomic characteristics, as well as unique results in comparative analysis of 16S rRNA gene sequence, OrthoANI, AAI, dDDH, and phylogenomic placement. Therefore, this strain represents a new species of the genus "Aliirhizobium", for which the name Aliirhizobium terrae sp. nov. is proposed, with the type strain is CC-CFT758T (= BCRC 81364T = JCM 35482T).

The impact of sampling time point on the lipidome composition.

Lipidomic profiling has been reported as an effective approach for characterizing and differentiating brain tumors. However, since lipids can undergo non-specific enzymatic and nonenzymatic reactions due to tissue disruption, it is critical to consider the preanalytical phase of the diagnostic process (e.g., optimizing the sampling time and sampling conditions). Thus, this study assesses the ways in which the time point of sampling impacts the lipidome composition of brain tumors. Two histologically distinct brain tumors-namely, meningiomas and gliomas-were sampled using solid-phase microextraction (SPME) fibers at two time points: on-site directly after removal, and after 12 months of storage at -30 °C. The samples were analyzed via HILIC chromatography coupled with HRMS, which enabled the detection of a wide range of features, including phospholipids and sphingolipids, as well as changes in the profiles of these compounds. The samples obtained from the stored tissues tended to have elevated levels of analytes with lower m/z values. In addition, the samples obtained from the fresh and stored tissues were easily distinguished based on their lipidome compositions, regardless of the histological tumor type. Notably, while storage did not affect the possibility of differentiating meningiomas and gliomas, the biological interpretation of the obtained results were prone to bias.

Functional genomics and taxonomic insights into heavy metal tolerant novel bacterium Brevibacterium metallidurans sp. nov. NCCP-602T isolated from tannery effluent in Pakistan.

The strain designated NCCP-602T was isolated from tannery effluent, and displayed aerobic, gram-positive, rod-shaped cells that were characterized by oxidase negative, catalase positive, and non-motile features. The most favourable growth conditions were observed at a temperature of 30°C, pH 7.0, and NaCl concentration of 1% (w/v). It tolerated heavy metals at high concentrations of chromium (3600 ppm), copper (3300 ppm), cadmium (3000 ppm), arsenic (1200 ppm) and lead (1500 ppm). The results of phylogenetic analysis, derived from sequences of the 16S rRNA gene, indicated the position of strain NCCP-602T within genus Brevibacterium and showed that it was closely related to Brevibacterium ammoniilyticum JCM 17537T. Strain NCCP-602 T formed a robust branch that was clearly separate from closely related taxa. A comparison of 16S rRNA gene sequence similarity and dDDH values between the closely related type strains and strain NCCP-602T provided additional evidence supporting the classification of strain NCCP-602T as a distinct novel genospecies. The polar lipid profile included diphosphatidylglycerol, glycolipid, phospholipids and amino lipids. MK-7 and MK-8 were found as the respiratory quinones, while anteiso-C15:0, iso-C15:0, iso-C16:0, iso-C17:0, and anteiso-C17:0 were identified as the predominant cellular fatty acids (> 10%). Considering the convergence of phylogenetic, phenotypic, chemotaxonomic, and genotypic traits, it is suggested that strain NCCP-602 T be classified as a distinct species Brevibacterium metallidurans sp. nov. within genus Brevibacterium with type strain NCCP-602T (JCM 18882T = CGMCC1.62055T).

A Comparative Study on the Composition and Structure of Human Milk Phospholipids and its Natural Resources: Based on a Similarity Evaluation Model.

Human milk phospholipids (HMPLs) play an indispensable role in the neurodevelopment and growth of infants. In this study, a total of 37 phospholipid fatty acid (PLFA) species and 139 phospholipid molecular species were detected from human milk and other natural phospholipid sources (including 5 animal-derived species and 2 plant species). Moreover, a similarity evaluation model for HMPLs was established, including phospholipid classes, PLFAs, and phospholipid molecular species, to evaluate their natural substitutes. The closest scores for HMPL substitute in these three dimensions was 0.89, 0.72, and 0.77, which belonged to mare milk, goat milk, and camel milk, respectively. The highest comprehensive similarity score was obtained by camel milk at 0.75, while the lowest score was observed in soybean phospholipid (0.22). Therefore, these results not only monitored the stereochemical structure of HMPLs and their substitutes, but also further provided new insights for the development of infant formulae.

LC-MS/MS-based phospholipid profiling of plant-pathogenic bacteria with tailored separation of methyl-branched species.

Plant-pathogenic bacteria are one of the major constraints on agricultural yield. In order to selectively treat these bacteria, it is essential to understand the molecular structure of their cell membrane. Previous studies have focused on analyzing hydrolyzed fatty acids (FA) due to the complexity of bacterial membrane lipids. These studies have highlighted the occurrence of branched-chain fatty acids (BCFA) alongside normal-chain fatty acids (NCFA) in many bacteria. As several FA are bound in the intact phospholipids of the bacterial membrane, the presence of isomeric FA complicates lipid analysis. Furthermore, commercially available reference standards do not fully cover potential lipid isomers. To address this issue, we have developed a reversed-phase high-performance liquid chromatography (RP-HPLC) method with tandem mass spectrometry (MS/MS) to analyze the phospholipids of various plant-pathogenic bacteria with a focus on BCFA containing phospholipids. The study revealed the separation of three isomeric phosphatidylethanolamines (PE) depending on the number of bound BCFA to NCFA. The validation of the retention order was based on available reference standards in combination with the analysis of hydrolyzed fatty acids through gas chromatography with mass spectrometry (GC/MS) after fractionation. Additionally, the transferability of the retention order to other major lipid classes, such as phosphatidylglycerols (PG) and cardiolipins (CL), was thoroughly examined. Using the information regarding the retention behavior, the phospholipid profile of six plant-pathogenic bacteria was structurally elucidated. Furthermore, the developed LC-MS/MS method was used to classify the plant-pathogenic bacteria based on the number of bound BCFA in the phospholipidome.

Phenylobacterium montanum sp. nov., an oligotrophic, slightly acidophilic mesophile isolated from sandy soil.

A bacterial strain, designated S6T, was isolated from the sandy soil on a rocky mountain in South China. Cells of S6T were Gram-stain-negative, aerobic, non-spore-forming, non-motile and non-prosthecae-producing. 16S rRNA gene sequence analysis revealed the highest similarities to 12 uncultured bacteria, followed by Phenylobacterium sp. B6.10-61 (97.14 %). The closest related validly published strains are Caulobacter henricii ATCC 15253T (96.15 %), Phenylobacterium conjunctum FWC 21T (96.08 %) and Caulobacter mirabilis FWC 38T (96.08 %). Phylogenetic analysis based on 16S rRNA gene, genome and proteome sequences demonstrated that S6T formed a separated lineage in the genus Phenylobacterium. Strain S6T contained Q-10 (97.5 %) as the major ubiquinone and C18 : 1 ω7c and C16 : 0 as the major fatty acids. The polar lipid profile consisted of phosphatidylglycerol, an unknown phosphoglycolipid and three unknown glycolipids. The assembled genome comprises a chromosome with a length of 5.5 Mb and a plasmid of 96 014 bp. The G+C content was 67.6 mol%. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus it is proposed that strain S6T represents a novel species in the genus Phenylobacterium, for which the name Phenylobacterium montanum sp. nov. is proposed. The type strain is S6T (=NBRC 115419T=GCMCC 1.18594T).