Analysis of cocoa products for ochratoxin A and aflatoxins

Eighty-five samples of cocoa products sampled in Canada were analysed for ochratoxin A (OTA) and aflatoxins in 2011–2012. Inclusion of the aflatoxins in this survey required additional method development. Chocolate was extracted with methanol–water plus NaCl, while for cocoa two successive extractions with methanol and methanol–water were made. Extracts were cleaned on an AflaOchra immunoaffinity column (IAC). Determination was by reversed phase high performance liquid chromatography (HPLC). Detection of the aflatoxins was with a post-column photochemical reactor and of OTA by fluorescence detection. Mean limits of quantification (LOQ) of chocolate and cocoa powders were 0.16 ng/g (OTA) and 0.07 ng/g (aflatoxin B₁), respectively. Survey results showed that the incidences of OTA above the LOQ in natural cocoa were 15/15 (mean 1.17 ng/g), 20/21 for alkalized cocoa (mean 1.06 ng/g), 9/9 for baking chocolate (mean 0.49 ng/g), 20/20 for dark chocolate (mean 0.39 ng/g), 7/10 for milk chocolate (mean 0.19 ng/g), 5/5 for cocoa liquor (mean 0.43 ng/g), and 0/5 for cocoa butter. These results confirm our previous work with OTA. In the same samples, incidences of aflatoxin B₁ above the LOQ were 14/15 for natural cocoa (mean 0.86 ng/g), 20/21 for alkalized cocoa (mean 0.37 ng/g), 7/9 for baking chocolate (mean 0.22 ng/g), 16/20 for dark chocolate (mean 0.19 ng/g), 7/10 for milk chocolate (mean 0.09 ng/g), 4/5 for cocoa liquor (mean 0.43 ng/g), and 0/5 for cocoa butter. Both aflatoxins and OTA were confirmed by HPLC-MS/MS when OTA or aflatoxin levels found were above 2 ng/g in cocoa.     

Mucor circinelloides whole-cells as a biocatalyst for the production of ethyl esters based on babassu oil

The intracellular lipase production by Mucor circinelloides URM 4182 was investigated through a step-by-step strategy to attain immobilized whole-cells with high lipase activity. Physicochemical parameters, such as carbon and nitrogen sources, inoculum size and aeration, were studied to determine the optimum conditions for both lipase production and immobilization in polyurethane support. Olive oil and soybean peptone were found to be the best carbon and nitrogen sources, respectively, to enhance the intracellular lipase activity. Low inoculum level and poor aeration rate also provided suitable conditions to attain high lipase activity (64.8 ± 0.8 U g^?1). The transesterification activity of the immobilized whole- cells was assayed and optimal reaction conditions for the ethanolysis of babassu oil were determined by experimental design. Statistical analysis showed that M. circinelloides whole-cells were able to produce ethyl esters at all tested conditions, with the highest yield attained (98.1 %) at 35 °C using an 1:6 oil-to-ethanol molar ratio. The biocatalyst operational stability was also assayed in a continuous packed bed reactor (PBR) charged with glutaraldehyde (GA) and Aliquat-treated cells revealing half-life of 43.0 ± 0.5 and 20.0 ± 0.8 days, respectively. These results indicate the potential of immobilized M. circinelloides URM 4182 whole-cells as a low-cost alternative to conventional biocatalysts in the production of ethyl esters from babassu oil.     

Analysis of a microbial community associated with polychlorinated biphenyl degradation in anaerobic batch reactors

The degradation of polychlorinated biphenyls (PCBs) was investigated under fermentative-methanogenic conditions for up to 60 days in the presence of anaerobic biomass from a full-scale UASB reactor. The low methane yields in the PCBs-spiked batch reactors suggested that the biomass had an inhibitory effect on the methanogenic community. Reactors containing PCBs and co-substrates (ethanol/sodium formate) exhibited substantial PCB reductions from 0.7 to 0.2 mg mL^?1. For the Bacteria domain, the PCBs-spiked reactors were grouped with the PCB-free reactors with a similarity of 55 %, which suggested the selection of a specific population in the presence of PCBs. Three genera of bacteria were found exclusively in the PCB-spiked reactors and were identified using pyrosequencing analysis, Sedimentibacter, Tissierela and Fusibacter. Interestingly, the Sedimentibacter, which was previously correlated with the reductive dechlorination of PCBs, had the highest relative abundance in the R_CS-PCB (7.4 %) and R_CS-PCB-PF (12.4 %) reactors. Thus, the anaerobic sludge from the UASB reactor contains bacteria from the Firmicutes phylum that are capable of degrading PCBs.     

Killing Rates for Caspofungin Against Candida albicans After Brief and Continuous Caspofungin Exposure in the Presence and Absence of Serum

It was previously demonstrated that brief (≤1 h) exposures to echinocandins are as effective to kill Candida albicans cells as continuous 24-h exposure. However, killing rates after continuous and short (1 h) echinocandin exposures to C. albicans have not yet been evaluated in RPMI-1640 with and without 50 % serum. We evaluated four echinocandin susceptible C. albicans bloodstream isolates, ATCC 10231 type strain and an echinocandin-resistant isolate (DPL20, FKS F645P). Caspofungin MICs, time-kill and postantifungal effect (PAFE) tests were performed in RPMI-1640 with and without 50 % serum. Killing rates (k values) in time-kill and PAFE experiments were determined for each strain and concentration. In time-kill experiments, colony count decreases were isolate- and concentration-dependent at 0.25, 1, 4, 8, 16 and 32 mg/L in RPMI-1640, but concentration-independent at 1, 4, 8, 16 and 32 mg/L in 50 % serum. One-hour caspofungin exposure at 4, 16 and 32 mg/L resulted in CFU decreases comparable with the results obtained in time-kill experiments in RPMI-1640, but 50 % serum at 4, 16 and 32 mg/L allowed growth of all isolates (k values were negative) (P < 0.05–0.001). PAFE in 50 % serum decreased markedly at 4, 16 and 32 mg/L. Killing rates remained high and concentration-independent in 50 % serum in case of continuous but not in case of brief caspofungin exposure. As only a short growth inhibition without killing was observed in 50 % serum, clinical relevance of caspofungin PAFE in vivo is questionable.     

Effect of the replacement of tropical forests with tree plantations on soil organic carbon levels in the Jomoro district,Ghana

Background and aims

In the Jomoro district in Ghana, tree plantations were the first cause of deforestation in the past, drastically reducing the area occupied by primary forests. The aim of this study was to quantify soil organic carbon (SOC) losses due to a change in land use from primary forest to tree plantations (cocoa, coconut, rubber, oil palm) on the different substrates of the district. Secondary forests and mixed plantations were also included in the study.

Methods

Soils were sampled at different depths up to 100 cm along a series of chronosequences in each of the three substrates (Granite, Lower Birrimian and Tertiary Sands) present in the area.

Results

The highest SOC losses in the 0–30 cm layer were caused by the conversion of primary forests to tree plantations: cocoa ?61 % of the original SOC stock, coconut ?55 %, rubber ?35 % and oil palm 28 %, while mixed plantations and secondary forests showed a loss of 23 % and 21 % of the original SOC stock, respectively. C losses were less apparent from the entire profile (to a depth of 100 cm).

Conclusions

All conversions to tree plantations caused substantial SOC losses, comparable to the conversion of forests to agricultural systems. Secondary forests and mixed plantations were the only sustainable land uses that restricted SOC losses considerably.     

Asymmetric synthesis of duloxetine intermediate (S)-(-)-3-N-methylamino-1-(2-thienyl)-1-propanol using immobilized Saccharomyces cerevisiae in liquid-core sodium alginate/chitosan/sodium alginate microcapsules

Duloxetine intermediate (S)-(-)-3-N-methylamino-1-(2-thienyl)-1-propanol was synthesized using ACA liquid-core immobilized Saccharomyces cerevisiae CGMCC No. 2230. The optimum culture time for ACA liquid-core immobilized cells was found to be 28 h. The optimum ACA liquid-core capsule formation conditions were found to be 90 % chitosan deacetylation, 30,000–50,000 chitosan molecular weight, 5.0 g/L chitosan, and pH 6.0 citrate buffer solution. The highest activity was found when reduction conditions were pH 6.0, 30 °C and 180 rpm. The ACA-immobilized cells can be reused nine times and only 40 % of the activity is retained after nine cycles. Product inhibition of reduction was observed in batch reduction. Continuous reduction in the membrane reactor was found to remove the product inhibition on reduction and improve production capacity. Conversion reached 100 % and enantiometric excess of (S)-(-)-3-N-methylamino-1-(2-thienyl)-1-propanol exceeded 99.0 % in continuous reduction of 5 g/L 3-N-methylamino-1-(2-thienyl)-1-propanone in the membrane reactor.     

Bacterial communities and greenhouse gas emissions of shallow ponds in the High Arctic

Permafrost thawing in lowland Arctic tundra results in a polygonal patterned landscape and the formation of numerous small ponds. These ponds emit biologically mediated carbon dioxide (CO₂) and methane (CH₄). Their greenhouse gas (GHG) emissions are variable, for reasons that are not well understood. Emissions are related to a balance between GHG producers and consumers, as well as to physical properties of the water column controlling gas exchange rates with the atmosphere. Here, we investigated the bacterial diversity of polygonal and runnel ponds, two geomorphologically distinct pond types commonly found in continuous permafrost regions. Using a combination of 16S rRNA Sanger sequencing and high-throughput amplicon sequencing, we found that bacterial communities in overlying waters were clearly dominated by carbon degraders and were similar in both pond types, despite their variable physical and chemical properties. However, surface sediment communities in the two pond types were significantly different. Polygonal pond sediment was colonized by carbon degraders (46–29 %), cyanobacteria (20–27 %) that take up CO₂ and produce oxygen, and methanotrophs (11–20 %) that consume CH₄ and require oxygen. In contrast, cyanobacteria were effectively absent from the surface sediment of runnel ponds, which in addition to carbon degraders (65–81 %), were colonized by purple non-sulfur bacteria (5–21 %), and by fewer methanotrophs (1–5 %). The link between the methanotrophic community and the type of ponds could potentially be used to improve upscale estimates of GHG emissions based on landscape morphology in such remote regions.     

Allergenic pollen in the atmosphere of Rohtak city,Haryana (India): a pioneer study

An attempt has been made in the present study to assess the allergenicity of dominant pollen types recorded from the atmosphere of Rohtak city. Skin prick test was performed with the antigenic extracts of 22 pollen types on 150 local patients who visited Asthma Clinic, University of Health Sciences, Rohtak. Markedly positive skin reactions (2+ and above) varied from 4.6 to 20.6 % to various pollen antigens. Cenchrus ciliaria (20.6 %), Zea mays (20 %) and Pennisetum typhoides (19.3 %) were the pollen allergens exhibiting maximum sensitivity. Antigenic extract of Cassia occidentalis, Cynodon dactylon and Ricinus communis showed marked skin reactivity in 18.6 % of patients. Prosopis juliflora, Chenopodium murale, Amaranthus spinosus, Cassia fistula and Cassia siamea showed 2+ and above reactions in 16.6, 15.3, 14.6 and 14.0 % of the local patients, respectively. Least reactivity (4.6 %) was shown to the antigenic extract of Cyperus rotundus. Out of 52 sera screened for the presence of specific IgE antibodies against different antigenic extracts, only 5.5 % showed >60 % binding. About 30 % and above binding was shown to the antigenic extracts of Z. mays, A. spinosus, R. communis and Xanthium strumarium. The concordance between positive skin reaction and serum-specific IgE antibodies ranged from 15 to 69 %.     

Effects of Icotinib on Advanced Non-Small Cell Lung Cancer with Different EGFR Phenotypes

Icotinib is the first oral epidermal growth factor receptor (EGFR) tyrosine kinase receptor inhibitor, which has been proven to exert significant inhibitory effects on non-small cell lung cancer in vitro. Clinical evidence has showed that the efficacy of Icotinib on retreating advanced non-small cell lung cancer is comparable to Gefitinib. However, different phenotypes of EGFR can affect the therapeutic outcomes of EGFR tyrosine kinase receptor inhibitor. Therefore, our study focused on efficacy and safety of Icotinib in patients with advanced non-small cell lung cancer of different EGPR phenotypes. Clinical data of patients with advanced non-small cell lung cancer who received Icotinib treatment from August, 2011 to May, 2013 were retrospectively analyzed. Kaplan–Meier analysis was used for survival analysis and comparison. 18 wild-type EGFR and 51 mutant type were found in a total of 69 patients. Objective response rate of patients with mutant type EGFR was 54.9 % and disease control rate was 86.3 %. Objective response rate of wild-type patients was 11.1 % (P = 0.0013 vs mutant type), disease control rate was 50.0 % (P = 0.0017). Median progression-free survival (PFS) of mutant type and wild-type patients were 9.7 and 2.6 months, respectively (P < 0.001). Median PFS of exon 19 mutated mutant patients was 11.3 months, mean PFS of exon 21 L858R mutated mutant patients was 8.7 months (P = 0.3145). Median overall survival (OS) of EGFR mutated patients had not reached. OS time of 13 wild-type patients was 12.9 months (P < 0.001). The common adverse reactions of Icotinib included rash, diarrhea, itching skin with occurrence rates of 24.6 % (17/69), 13.0 % (9/69), and 11.6 % (8/69), respectively. Most adverse reactions were grade I–II. Icotinib has great efficacy in EGFR mutated patients, making it an optimal regimen to treat EGFR mutated patients. Furthermore, most of adverse reactions associated with Icotinib treatment were tolerable.     

Association of vitamin D receptor FokI and ApaI polymorphisms with lung cancer risk in Tunisian population

Many studies reported that Vitamin D Receptor (VDR) gene polymorphisms might influence the cancer risk due to their antiproliferative, antiangiogenic, and apoptotic effects. The aim of this study was to explore the genetic association of VDR polymorphisms with lung cancer risk in Tunisian population. The genotype and haplotype frequencies of four VDR polymorphisms, FokI (rs2228570), BsmI (rs1544410), ApaI (rs7975232) and TaqI (rs731236) were studied using polymerase chain reaction and restriction fragment length polymorphism analysis in 240 patients with lung cancer and 280 healthy controls. The distribution of genotype frequencies differed significantly between lung cancer subjects and controls (FokI P _adj  = 0.002; ApaI P _adj  = 0.013). Haplotype analyses revealed a significant association between G-A-C and A-C-T haplotypes and lung cancer risk (P _corr  = 0.0128, P _corr  = 0.008). When patients were stratified according to gender, age, and smoking, significant associations were detected with FokI and TaqI polymorphisms. We found a lack of association between BsmI, TaqI polymorphisms and lung cancer risk (P > 0.05). Only, the attributable proportion due to interaction and the synergic index for interaction between ApaI polymorphism and smoking were statistically significant (P _adj  = 0.74, 95 % CI = 0.38–1.20) and (P _adj  = 0.63, 95 % CI = 0.05–1.21), respectively. Both the additive interaction measures suggested the existence of a biological interaction between SNP ApaI, but not FokI, and smoking. The multiplicative interaction measure was not statistically significant (P > 0.05). This is the first study in Tunisia, which suggested that VDR FokI and ApaI polymorphisms might be risk factors for lung cancer development.     

Simplified feeding strategies for the fed-batch cultivation of Kluyveromyces lactis GG799 for enhanced recombinant xylanase production

A xylanase gene (xyn2) from Trichoderma reesei ATCC 58350 was previously cloned and expressed in Kluyveromyces lactis GG799. The production of the recombinant xylanase was conducted in a developed medium with an optimised batch and with fed-batches that were processed with glucose. The glucose served as a carbon source for cell growth and as an inducer for xylanase production. In a 1-L batch system, a glucose concentration of 20 g L^?1 and 80 % dissolved oxygen were found to provide the best conditions for the tested ranges. A xylanase activity of 75.53 U mL^?1 was obtained. However, in the batch mode, glucose depletions reduced the synthesis of recombinant xylanase by K. lactis GG799. To maximise the production of xylanase, further optimisation was performed using exponential feeding. We investigated the effects of various nitrogen sources combined with the carbon to nitrogen (C/N) molar ratio on the production of xylanase. Of the various nitrogen sources, yeast extract was found to be the most useful for recombinant xylanase production. The highest xylanase production (110.13 U mL^?1) was measured at a C/N ratio of 50.08. These conditions led to a 45.8 % increase in xylanase activity compared with the batch cultures. Interestingly, the further addition of 500 g L^?1 glucose led to a 6.2-fold increase (465.07 U mL^?1) in recombinant xylanase activity. These findings, together with those of the exponential feeding strategy, indicate that the composition of the C/N molar ratio has a substantial impact on recombinant protein production in K. lactis.     

Broadband Reflection Minimization Using Silver Ultra Thin Film Sandwiched Between Silicon Nitride Layers for c-Si Solar Cell Application

Wafer thickness reduction is the main trend for cost reduction of crystalline silicon (c-Si) solar cells. For better light trapping in lower thickness wafers where traditional texturization method may not be promising, alternative techniques are being explored. Here, reflection minimization using silver ultra thin film sandwiched between silicon nitride (SiN_x) antireflection coating (ARC) layers on c-Si substrate is reported. SiN_x ARC layers were deposited by plasma-enhanced chemical vapor deposition (PECVD) and silver ultra thin film by e-beam evaporation; 41 % reflection reduction for silver ultra thin film sandwiched in SiN_x ARC layers as compared to standard 80 nm thin SiN_x ARC on c-Si substrate is shown. The sandwiched structure gives 8.1 % weighted total reflectance for wavelength range of 300–1,200 nm as compared to standard 80-nm SiN_x-based ARC which gives 13.8 %. Also, comparison of this Ag ultra thin film-based sandwiched geometry is done with randomly distributed nanoparticle (NP)-based ARC geometry. It is shown that optically, the sandwiched Ag ultra thin film-based device geometry is more promising than Ag NP-based device geometry and standard 80-nm SiN_x-based geometry for broad wavelength range of 300–1,200 nm.     

Identification of methylation quantitative trait loci (mQTLs) influencing promoter DNA methylation of alcohol dependence risk genes

Interaction of DNA methylation and sequence variants that are methylation quantitative trait loci (mQTLs) may influence susceptibility to diseases such as alcohol dependence (AD). We used genome-wide genotype data from 268 African Americans (AAs: 129 AD cases and 139 controls) and 143 European Americans (EAs: 129 AD cases and 14 controls) to identify mQTLs that were associated with promoter CpGs in 82 AD risk genes. 282 significant mQTL–CpG pairs (9.9 × 10^?100 ≤ P _nominal ≤ 7.7 × 10^?8) in AAs and 313 significant mQTL–CpG pairs (2.7 × 10^?53 ≤ P _nominal ≤ 9.9 × 10^?8) in EAs were identified [i.e., mQTL–CpG associations survived multiple-testing correction, q values (false discovery rate) ≤ 0.05]. The most significant mQTL was rs1800759, which was strongly associated with CpG cg12011299 in both AAs (P _nominal = 9.9 × 10^?100; q = 6.7 × 10^?91) and EAs (P _nominal = 2.7 × 10^?53; q = 1.4 × 10^?44). Rs1800759 (previously known to be associated to AD) and CpG cg12011299 (distance: 37 bp) are both located in alcohol dehydrogenase (ADH) 4 gene (ADH4) promoter region. In general, the strength of association between mQTLs and CpGs was inversely correlated with the distance between them. Association was also influenced by race and AD. Additionally, 48.3 % of the mQTLs identified in AAs and 65.6 % of the mQTLs identified in EAs were predicted to be expression QTLs. Three mQTLs (rs2173201, rs4147542, and rs4147541 in ADH1B-AHD1C gene cluster region) found in AAs were previously identified by our genome-wide association studies as being significantly associated with AD in AAs. Thus, DNA methylation, which can be influenced by sequence variants and is implicated in gene expression regulation, appears to at least partially underlie the association of genetic variation with AD.     

Quantitative Assessment of the Association Between HDMX Polymorphism and Sarcoma

To investigate the effects of the HDMX polymorphism on sarcoma risk. Relevant studies were identified by searching the PubMed, Embase, and Web of Science databases. Data were extracted by two independent investigators. Odds ratios (ORs) and 95 % confidence intervals (CIs) were calculated using a fixed-effects model to assess the association between the HDMX polymorphism and sarcoma risk. We also conducted heterogeneity test, sensitivity analysis, and publication bias test. A meta-analysis of four published case–control studies involving 1,115 subjects (379 cases and 736 controls) showed no statistical association between the HDMX polymorphism and sarcoma risk (OR_{TT vs. GG}  0.88, 95 % CI  0.68–1.14, P _{heterogeneity}  0.819; OR_{TT + TG vs. GG} 0.95, 95 % CI  0.79–1.15, P _{heterogeneity}  0.937; OR_{TT vs. TG + GG}  0.82, 95 % CI  0.65–1.04, P _{heterogeneity}  0.589; OR_{T allele vs. G allele}  0.91, 95 % CI  0.79–1.05, P _{heterogeneity}  0.727; OR_{TG vs. GG}  0.95, 95 % CI  0.74–1.22, P _{heterogeneity} = 0.869). This null result did not alter when data were stratified according to ethnicity. Our meta-analysis indicates that the HDMX polymorphism is unlikely to contribute to individual susceptibility to sarcoma.     

Hydraulic adjustments in aspen (Populus tremuloides) seedlings following defoliation involve root and leaf aquaporins

Main conclusion

Changes in root and leaf hydraulic properties and stimulation of transpiration rates that were initially triggered by defoliation were accompanied by corresponding changes in leaf and root aquaporin expression. Aspen (Populus tremuloides) seedlings were subjected to defoliation treatments by removing 50, 75 % or all of the leaves. Root hydraulic conductivity (L_pr) was sharply reduced in plants defoliated for 1 day and 1 week. The decrease in L _pr could not be prevented by stem girdling and it was accompanied in one-day-defoliated plants by a large decrease in the root expression of PIP1,2 aquaporin and an over twofold decrease in hydraulic conductivity of root cortical cells (L _pc). Contrary to L _pr and L _pc, 50 and 75 % defoliation treatments profoundly increased leaf lamina conductance (K _lam) after 1 day and this increase was similar in magnitude for both defoliation treatments. Transpiration rates (E) rapidly declined after the removal of 75 % of leaves. However, E increased by over twofold in defoliated plants after 1 day and the increases in E and K _lam were accompanied by five- and tenfold increases in the leaf expression of PIP2;4 in 50 and 75 % defoliation treatments, respectively. Defoliation treatments also stimulated net photosynthesis after 1 day and 3 weeks, although the increase was not as high as E. Leaf water potentials remained relatively stable following defoliation with the exception of a small decrease 1 day after defoliation which suggests that root water transport did not initially keep pace with the increased transpirational water loss. The results demonstrate the importance of root and leaf hydraulic properties in plant responses to defoliation and point to the involvement of PIP aquaporins in the early events following the loss of leaves.     

The Role of the rs1544410 Polymorphism of Vitamin D Receptor Gene in Breast Cancer Susceptibility

This study was devised to investigate the genetic effect modification of the BsmI polymorphism associated with the susceptibility to breast cancer. Case–control studies of the BsmI polymorphism and breast cancer were searched. A total of 17 eligible publications were included in our final analysis. Pooled ORs and 95 % CIs were obtained by means of fixed effects model. The general and stratified analyses according to ethnicity showed that the association between the BsmI polymorphism and the risk of breast cancer was not statistically significant. However, the subgroup of the hospital-based studies was found to confer protection against the disease (OR_BBvs.bb = 0.83, 95 % CI = 0.71–0.97, P _h = 0.571; OR_BBvs.Bb+bb = 0.86, 95 % CI = 0.74–1.00, P _h = 0.903; OR_{allele B vs. allele b} = 0.92, 95 % CI = 0.86–0.99, P _h = 0.337). Our results suggested that the presence of the BsmI polymorphism may contribute to the susceptibility of breast cancer. It is necessary that future large-scale studies should be conducted to further confirm the association between the BsmI polymorphism and breast cancer risk.     

Pelagibaca abyssi sp. nov., of the family Rhodobacteraceae,isolated from deep-sea water

A Gram-stain negative, oval-shaped, aerobic, catalase and oxidase-positive bacterium, designated JLT2014^T, was isolated from a deep-seawater sample (obtained at a 2,000 m depth) of the Southeastern Pacific Ocean. The dominant fatty acids were identified as C_18:1ω7c/C_18:1ω6c, C_16:0 and C_10:0 3-OH, which altogether represented 60.1 % of the total. The predominant respiratory quinone was identified as Q-10. The G+C content of genomic DNA was determined to be 66.4 mol %. The major polar lipids were identified as phosphatidylethanolamine and diphosphatidylglycerol. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the novel isolate can be affiliated with the Roseobacter clade within the family Rhodobacteraceae. Strain JLT2014^T exhibited highest 16S rRNA gene sequence similarity value to Pelagibaca bermudensis HTCC2601^T (sequence similarity value: 97.6 %). The DNA–DNA relatedness value between strain JLT2014^T and P. bermudensis HTCC2601^T was 46.9 ± 2 %. Based on phenotypic properties and phylogenetic analysis, the name Pelagibaca abyssi sp. nov. is proposed, with JLT2014^T(=LMG 27363^T=CGMCC 1.12376^T) as the type strain.     

Paenibacillus abyssi sp. nov., isolated from an abyssal sediment sample from the Indian Ocean

A Gram-positive, rod-shaped bacterium, designated strain SCSIO N0306^T, was isolated from an abyssal sediment sample collected from the Indian Ocean. The isolate was found to grow optimally at 0–2 % (w/v) NaCl, pH 7.0 and 30 °C. Comparative analysis of the 16S rRNA gene sequence showed that the isolate SCSIO N0306^T belongs phylogenetically to the genus Paenibacillus, and to be most closely related to P. algorifonticola XJ259^T (with 95.47 % sequence similarity), sharing less than 95.0 % sequence similarity with all other taxa of this genus. Chemotaxonomic analysis revealed MK-7 as the major isoprenoid quinone, the DNA G+C content was determined to be 45.5 mol%, and anteiso-C_15:0, C_16:0, and iso-C_15:0 were identified as the major fatty acids. On the basis of this polyphasic taxonomic data, isolate SCSIO N0306^T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus abyssi sp. nov. is proposed. The type strain is SCSIO N0306^T (= DSM 26238^T = CGMCC 1.12987^T).