Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean.

Ammonia oxidation to nitrite and its subsequent oxidation to nitrate provides energy to the two populations of nitrifying chemoautotrophs in the energy-starved dark ocean, driving a coupling between reduced inorganic nitrogen (N) pools and production of new organic carbon (C) in the dark ocean. However, the relationship between the flux of new C production and the fluxes of N of the two steps of oxidation remains unclear. Here, we show that, despite orders-of-magnitude difference in cell abundances between ammonia oxidizers and nitrite oxidizers, the two populations sustain similar bulk N-oxidation rates throughout the deep waters with similarly high affinities for ammonia and nitrite under increasing substrate limitation, thus maintaining overall homeostasis in the oceanic nitrification pathway. Our observations confirm the theoretical predictions of a redox-informed ecosystem model. Using balances from this model, we suggest that consistently low ammonia and nitrite concentrations are maintained when the two populations have similarly high substrate affinities and their loss rates are proportional to their maximum growth rates. The stoichiometric relations between the fluxes of C and N indicate a threefold to fourfold higher C-fixation efficiency per mole of N oxidized by ammonia oxidizers compared to nitrite oxidizers due to nearly identical apparent energetic requirements for C fixation of the two populations. We estimate that the rate of chemoautotrophic C fixation amounts to ∼1 × 1013 to ∼2 × 1013 mol of C per year globally through the flux of ∼1 × 1014 to ∼2 × 1014 mol of N per year of the two steps of oxidation throughout the dark ocean.

Acuticoccus yangtzensis gen. nov., sp. nov., a novel member in the family Rhodobacteraceae, isolated from the surface water of the Yangtze Estuary.

A novel bacterium, strain JL1095(T), was isolated from the surface water of the Yangtze Estuary, China (31° N, 122° E). Cells were Gram negative, aerobic, oval-shaped with one peak end and motile by gliding. Cells divided by binary fission. Growth occurred at 15-50 °C (optimum at 35 °C), 2-10 % (w/v) NaCl (optimum at ~3 %) and pH 6.0-9.0 (optimum at pH ~ 7.6). Strain JL1095(T) was able to utilize various sole-carbon-source, such as Tween 40, Tween 80, acetic acid, L-arabinose, D,L-lactic acid, urocanic acid, methyl-pyruvate, α-hydroxy butyric acid, ß-hydroxy butyric acid, and γ-hydroxy butyric acid. The major cellular fatty acids were C16:0, C18:0, C19:0 ω8c cyclo, C20:1 ω7c, and Summed Feature 8. The whole respiratory ubiquinone was Q-10. The genomic DNA G+C content of strain JL1095(T) was 51.5 %. According to the phylogenetic analysis, strain JL1095(T) formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genera Labrenzia, Pannonibacter, Stappia, Wenxnia, and Amaricoccus. The sequence similarity was 92.8 % with the most closely relating strain Stappia indica B106(T), and 92.6 % with the type species Stappia stellulatum IAM 12621(T). Based on the biochemical characteristics, chemotaxonomy and phylogenetic analysis, strain JL1095(T) is considered to be a novel genus which belongs to the family Rhodobacteraceae. The novel strain is named Acuticoccus yangtzensis gen. nov., sp. nov. The type strain of Acuticoccus yangtzensis is JL1095(T) (=CGMCC 1.12795 = DSM 28604).

Influence of different polymers on crystallization tendency and dissolution behavior of cilnidipine in solid dispersions.

CONTEXT: Cilnidipine (CN) is a novel dihydropyridine calcium antagonist that is practically insoluble in aqueous media and exhibits a low oral bioavailability or limited clinical efficacy. OBJECTIVE: This study investigated the effects of three commercial and chemically diverse polymers - PVP, PVP/VA and Soluplus - on crystallization tendency and in vitro dissolution profiles of CN in order to determine an optimum carrier for composing the preferred solid dispersion (SD) of CN. METHODS: All these co-evaporated systems were characterized up to 3 months by thermoanalytical (DSC), crystallographic (POM, PXRD), microscopic (SEM) and spectroscopic (FTIR) techniques. RESULTS: The results showed that the polymers could be sorted by their effects of inhibiting CN crystallization in the ascending order: Soluplus, PVP/VA, PVP. The sequence was in accordance with that of the strength of drug-polymer hydrogen bonds revealed by FTIR spectra. It could be ascribed to relative hydrogen-bonding acceptor strengths of N-vinylpyrrolidone moiety in the polymer molecules. On the other hand, all the SDs showed enhanced dissolution profiles compared to pure CN alone. On their effects of enhancing CN dissolution, the polymers could be sorted in the descending order: Soluplus, PVP, PVP/VA. CONCLUSIONS: It implied that the dissolution behavior of CN could bear a close relationship to both hydration capacity and hydrogen-bonding interaction tendency of moieties of the polymers. It might suggest an optimal formulation for CN comprising both PVP and Soluplus.

Euryhalocaulis caribicus gen. nov., sp. nov., a new member [corrected] of the family Hyphomonadaceae isolated from the Caribbean Sea.

A new aerobic, Gram-negative, chemo-organotrophic, euryhaline bacterium, designated strain JL2009(T), was isolated from surface water of the Caribbean Sea. The strain formed flaxen colonies on marine ager 2216 (MA; Difco) medium. Cells were dimorphic, with stalks or a polar flagellum, and reproduction occurred by means of binary fission. Growth occurred at 15-45 °C (optimum at 35 °C), 0-15 % (w/v) NaCl (optimum at 1-10 %) and pH 5-9 (optimum at pH 7-8). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain formed a distinct evolutionary lineage within the family Hyphomonadaceae. Strain JL2009(T) was most closely related to Maricaulis parjimensis MCS 25(T) (92.2 % DNA sequence similarity), Woodsholea maritime CM2243(T) (90.9 %), and Oceanicaulis alexandrii C116-18(T) (90.9 %). The major respiratory quinone was Q-10. The dominant cellular fatty acids were summed feature 8 (C(18:1) ω7c), C(18:0) and 11-methyl C(18:1) ω7c. The polar lipid pattern indicated the presence of phospholipid, phosphatidyl glycerol and glycolipids. The G + C content of the genomic DNA was 70.5 mol%. On the basis of the chemotaxonomic and phenotypic characteristics and the phylogenetic evidence, strain JL2009(T) represents a novel genus and species in the family Hyphomonadaceae, for which the name Euryhalocaulis caribicus gen. nov., sp. nov. is proposed. The type strain of Euryhalocaulis caribicus is JL2009(T) (=CGMCC 1.12036(T) = JCM 18163(T)).

Rapid screening and quantification of sulfonate derivatives in white peony root by UHPLC-MS-MS.

A rapid ultra-high-performance liquid chromatographic-tandem mass spectrometric (UHPLC-MS-MS) method has been developed for rapid screening and quantitative analysis of sulfonate derivatives (SDs) in commercial white peony root. Separation was performed on an Agilent Zorbax Eclipse Plus-C18 column by gradient elution with acetonitrile-0.1% (v/v) formic acid as the mobile phase. In-source fragmentation was used to generate the characteristic fragment ion at m/z 259 and to screen for nine SDs. Detection of these SDs was further performed in multiple reaction monitoring (MRM) mode to improve sensitivity and to quantify the two SDs paeoniflorin sulfonate and benzoylpaeoniflorin sulfonate. The method was validated for specificity, linearity, limits of detection and quantification, precision, accuracy, and matrix effects. Nine commercial white peony root samples were examined by use of this method, which revealed great variety in the paeoniflorin sulfonate and benzoylpaeoniflorin sulfonate content.

Coupled Carbon, Sulfur, and Nitrogen Cycles Mediated by Microorganisms in the Water Column of a Shallow-Water Hydrothermal Ecosystem.

Shallow-water hydrothermal vent ecosystems are distinctly different from deep-sea vents, as other than geothermal, sunlight is one of their primary sources of energy, so their resulting microbial communities differ to some extent. Yet compared with deep-sea systems, less is known about the active microbial community in shallow-water ecosystems. Thus, we studied the community compositions, their metabolic pathways, and possible coupling of microbially driven biogeochemical cycles in a shallow-water hydrothermal vent system off Kueishantao Islet, Taiwan, using high-throughput 16S rRNA sequences and metatranscriptome analyses. Gammaproteobacteria and Epsilonbacteraeota were the major active bacterial groups in the 16S rRNA libraries and the metatranscriptomes, and involved in the carbon, sulfur, and nitrogen metabolic pathways. As core players, Thiomicrospira, Thiomicrorhabdus, Thiothrix, Sulfurovum, and Arcobacter derived energy from the oxidation of reduced sulfur compounds and fixed dissolved inorganic carbon (DIC) by the Calvin-Benson-Bassham (CBB) or reverse tricarboxylic acid cycles. Sox-dependent and reverse sulfate reduction were the main pathways of energy generation, and probably coupled to denitrification by providing electrons to nitrate and nitrite. Sulfur-reducing Nautiliaceae members, accounting for a small proportion in the community, obtained energy by the oxidation of hydrogen, which also supplies metabolic energy for some sulfur-oxidizing bacteria. In addition, ammonia and nitrite oxidation is another type of energy generation in this hydrothermal system, with marker gene sequences belonging to Thaumarchaeota/Crenarchaeota and Nitrospina, respectively, and ammonia and nitrite oxidation was likely coupled to denitrification by providing substrate for nitrate and nitrite reduction to nitric oxide. Moreover, unlike the deep-sea systems, cyanobacteria may also actively participate in major metabolic pathways. This study helps us to better understand biogeochemical processes mediated by microorganisms and possible coupling of the carbon, sulfur, and nitrogen cycles in these unique ecosystems.

Genome sequence of Acuticoccus yangtzensis JL1095T (DSM 28604T) isolated from the Yangtze Estuary.

Acuticoccus yangtzensis JL1095T is a proteobacterium from a genus belonging to the family Rhodobacteraceae; it was isolated from surface waters of the Yangtze Estuary, China. This strain displays the capability to utilize aromatic and simple carbon compounds. Here, we present the genome sequence, annotations, and features of A. yangtzensis JL1095T. This strain has a genome size of 5,043,263 bp with a G + C content of 68.63%. The genome contains 4286 protein-coding genes, 56 RNA genes, and 83 pseudo genes. Many of the protein-coding genes were predicted to encode proteins involved in carbon metabolism pathways, such as aromatic degradation and methane metabolism. Notably, a total of 31 genes were predicted to encode form II carbon monoxide dehydrogenases, suggesting potential for carbon monoxide oxidation. The genome analysis helps better understand the major carbon metabolic pathways of this strain and its role in carbon cycling in coastal marine ecosystems.

Differential Incorporation of Carbon Substrates among Microbial Populations Identified by Field-Based, DNA Stable-Isotope Probing in South China Sea.

To determine the adapted microbial populations to variant dissolved organic carbon (DOC) sources in the marine environment and improve the understanding of the interaction between microorganisms and marine DOC pool, field-based incubation experiments were carried out using supplemental 13C-labeled typical substrates D-glucose and D-glucosamine (D-Glc and D-GlcN, respectively), which are two important components in marine DOC pool in the South China Sea. 13C- and 12C-DNA were then fractionated by ultracentrifugation and the microbial community was analyzed by terminal-restriction fragment length polymorphism and 454 pyrosequencing of 16S rRNA gene. 12C-DNA-based communities showed relatively high similarities with their corresponding in situ communities, and their bacterial diversities were generally higher than 13C-DNA-based counterparts. Distinct differences in community composition were found between 13C- and 12C-DNA-based communities and between two substrate-supplemented 13C-DNA-based communities; these differences distinctly varied with depth and site. In most cases, there were more genera with relative abundances of >0.1% in D-Glc-incorporating communities than in D-GlcN-incorporating communities. The Roseobacter clade was one of the prominent actively substrate-incorporating bacterial populations in all 13C-DNA-based communities. Vibrio was another prominent actively D-GlcN-incorporating bacterial population in most incubations. However notably, different OTUs dominated this clade or genus in different treatments at different depths. Altogether, these results suggested that there were taxa-specific differences in DOC assimilations and, moreover, their differences varied among the typical water masses, which could have been caused by the variant compositions of original bacterial communities from different hydrological environments. This implies that ecologically, the levels of labile or recalcitrance of DOC can be maintained only in a specific environmental context with specific bacterial community composition.

Draft Genome Sequence of Euryhalocaulis caribicus Strain JL2009T, a New Member of the Family Hyphomonadaceae Isolated from the Caribbean Sea.

Euryhalocaulis caribicus strain JL2009(T) is a novel genus and species of the family Hyphomonadaceae and was first isolated from surface water in the Caribbean Sea. Here, we report the first draft genome from this genus. Its genome contains genes encoding proteins that are involved in organic acid metabolism and probable low-affinity inorganic phosphate transporters, which suggests its competence in oligotrophic oceans.