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[PMID]:28744579
[Au] Autor:Uda K; Abe K; Dehara Y; Mizobata K; Edashige Y; Nishimura R; Radkov AD; Moe LA
[Ad] Endereço:Laboratory of Biochemistry, Faculty of Science and Technology, Kochi University, Kochi, 780-8520, Japan. k-uda@kochi-u.ac.jp.
[Ti] Título:Triple serine loop region regulates the aspartate racemase activity of the serine/aspartate racemase family.
[So] Source:Amino Acids;49(10):1743-1754, 2017 10.
[Is] ISSN:1438-2199
[Cp] País de publicação:Austria
[La] Idioma:eng
[Ab] Resumo:Recently, we cloned and characterized eleven serine and aspartate racemases (SerR and AspR, respectively) from animals. These SerRs and AspRs are not separated by their racemase functions and form a serine/aspartate racemase family cluster based on phylogenetic analysis. Moreover, we have proposed that the AspR-specific triple serine loop region at amino acid positions 150-152 may be responsible for the large AspR activity. In the present study, to test this hypothesis, we prepared and characterized fourteen mutants in this region of animal SerRs and AspRs. The large AspR activity in Acropora and Crassostrea AspR was reduced to <0.04% of wild-type after substitution of the triple serine loop region. Conversely, introducing the triple serine loop region into Acropora, Crassostrea, and Penaeus SerR drastically increased the AspR activity. Those mutants showed similar or higher substrate affinity for aspartate than serine and showed 11-683-fold higher k and 28-351-fold higher k /K values for aspartate than serine racemization. Furthermore, we introduced serine residues in all combinations at position 150-152 in mouse SerR. These mutants revealed that a change in the enzyme function from SerR to AspR can be caused by introduction of Ser151 and Ser152, and addition of the third serine residue at position 150 further enhances the enzyme specificity for aspartate due to a decrease in the serine racemase and serine dehydratase activity. Here, we provide convincing evidence that the AspR gene has evolved from the SerR gene by acquisition of the triple serine loop region.
[Mh] Termos MeSH primário: Isomerases de Aminoácido
Antozoários
Proteínas de Artrópodes
Crassostrea
Mutação de Sentido Incorreto
Penaeidae
Racemases e Epimerases
[Mh] Termos MeSH secundário: Isomerases de Aminoácido/química
Isomerases de Aminoácido/genética
Substituição de Aminoácidos
Animais
Antozoários/enzimologia
Antozoários/genética
Proteínas de Artrópodes/química
Proteínas de Artrópodes/genética
Crassostrea/enzimologia
Crassostrea/genética
Camundongos
Penaeidae/enzimologia
Penaeidae/genética
Estrutura Secundária de Proteína
Racemases e Epimerases/química
Racemases e Epimerases/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Arthropod Proteins); EC 5.1.- (Racemases and Epimerases); EC 5.1.1.- (Amino Acid Isomerases); EC 5.1.1.13 (aspartate racemase); EC 5.1.1.16 (serine racemase)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180305
[Lr] Data última revisão:
180305
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170727
[St] Status:MEDLINE
[do] DOI:10.1007/s00726-017-2472-8


  2 / 1106 MEDLINE  
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[PMID]:29277610
[Au] Autor:Liu H; Xu D; Cui M; Hou T; Zhang Q
[Ad] Endereço:Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, J
[Ti] Título:The transcriptional factor YB-1 positively regulates Hsc70 transcription in Crassostrea hongkongensis.
[So] Source:Biochem Biophys Res Commun;495(4):2404-2409, 2018 01 22.
[Is] ISSN:1090-2104
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:A Y-box binding protein ChYB-1 was discovered as a ChHsc70 promoter-associated protein in Crassostrea hongkongensis by DNA-affinity purification and mass spectrometry analysis. The overexpression of ChYB-1 in heterologous HEK293T cells led to clear enhancement of ChHsc70 promoter expression, while ChYB-1 depletion correlated with significant reduction of ChHsc70 transcription in the hemocytes of C. hongkongensis. Quantitative Real-time PCR analysis revealed that both ChHsc70 and ChYB-1 were transcriptionally responsive to external chemical or physical stressors. This indicates a plausible correlation between ChHsc70 and ChYB-1 in the genetic regulatory pathway triggered by external stresses. This study presents the first evidence of positive regulator for Hsc70 transcription and contributes to a better understanding of the regulatory mechanisms governing Hsc70 expression.
[Mh] Termos MeSH primário: Crassostrea/metabolismo
Regulação da Expressão Gênica/fisiologia
Proteínas de Choque Térmico HSC70/metabolismo
Fatores de Transcrição/metabolismo
Ativação Transcricional/fisiologia
Proteína 1 de Ligação a Y-Box/metabolismo
[Mh] Termos MeSH secundário: Animais
Estresse Oxidativo/fisiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (HSC70 Heat-Shock Proteins); 0 (Transcription Factors); 0 (Y-Box-Binding Protein 1)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180222
[Lr] Data última revisão:
180222
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171227
[St] Status:MEDLINE


  3 / 1106 MEDLINE  
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[PMID]:29176846
[Au] Autor:Hu S; Zhao G; Zheng Y; Qu M; Jin Q; Tong C; Li W
[Ad] Endereço:College of Food Science and Engineering, Dalian Ocean University, Dalian, P. R. China.
[Ti] Título:Effect of drying procedures on the physicochemical properties and antioxidant activities of polysaccharides from Crassostrea gigas.
[So] Source:PLoS One;12(11):e0188536, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Crassostrea gigas polysaccharides (CGP) were obtained by different drying methods: freeze-drying (FD), spray-drying (SD) or rotary evaporation-drying (RED). The physicochemical properties of CGP were evaluated on the basis of polysaccharide content, protein content, color characteristics, FT-IR spectroscopy, differential scanning calorimetry (DSC), and scanning electron microscopy (SEM). Antioxidant activities were researched three different free radicals, including DPPH free radicals, ABTS free radicals and reducing power. The results demonstrated that FDCGP, SDCGP and REDCGP have different physicochemical properties and antioxidant activities. Contrasted with FDCGP and REDCGP, SDCGP exhibited stronger antioxidant abilities. Therefore, considering the polysaccharides appearances and antioxidant activities, the spray drying method is a decent selection for the preparation of such polysaccharides, and it should be selected for application in the food industry.
[Mh] Termos MeSH primário: Antioxidantes/farmacologia
Crassostrea/metabolismo
Polissacarídeos/farmacologia
[Mh] Termos MeSH secundário: Animais
Varredura Diferencial de Calorimetria
Cor
Microscopia Eletrônica de Varredura
Espectrofotometria Ultravioleta
Espectroscopia de Infravermelho com Transformada de Fourier
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Antioxidants); 0 (Polysaccharides)
[Em] Mês de entrada:1712
[Cu] Atualização por classe:171226
[Lr] Data última revisão:
171226
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171128
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0188536


  4 / 1106 MEDLINE  
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[PMID]:28454761
[Au] Autor:Kim JH; Jeong SY; Kim PJ; Dahms HU; Han KN
[Ad] Endereço:Unit of Polar Genomics, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, South Korea.
[Ti] Título:Bio-effect-monitoring of long-term thermal wastes on the oyster, Crassostrea gigas, using heat shock proteins.
[So] Source:Mar Pollut Bull;119(1):359-364, 2017 Jun 15.
[Is] ISSN:1879-3363
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:We bio-monitored the stress of oyster, Crassostrea gigas, for possible long term effects of thermal waste from a power plant. The expression level of its heat shock proteins (HSPs) was measured by real time-reverse transcript PCR along with their density and growth in the field. Oyster size varied in a distance dependent pattern. Physics modeling for evaluation of spreading of the thermal effluent revealed that station A is affected by the thermal effluents abundance, and the size of C. gigas showed a negative relationship with distance to the power plant. The abundance and size of C. gigas were smallest at station A, which was closest to the thermal effluent outlet. The kinetics of changes in the hsp70 and hsp90 mRNA levels in the mantle of C. gigas were also investigated. Regardless of the higher expression level of hsp70 mRNA than hsp90, both hsp70 and hsp90 mRNA levels were significantly higher at station A. The expression levels decreased inversely with distance from the thermal effluent outlet, with expression of hsp70 mRNA at station A being approximately 7-fold higher than at station B and 15-fold higher than at station C. Similarly, expression of hsp90 mRNA at station A was approximately 14-fold higher than at station B and 22-fold higher than at station C. The present findings provide new insights on biological correlation among the growth of individuals and population size and the molecular index in C. gigas following thermal effects.
[Mh] Termos MeSH primário: Crassostrea
Monitoramento Ambiental/métodos
Proteínas de Choque Térmico/metabolismo
Temperatura Ambiente
[Mh] Termos MeSH secundário: Animais
Proteínas de Choque Térmico HSP70
RNA Mensageiro
Estresse Fisiológico
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (HSP70 Heat-Shock Proteins); 0 (Heat-Shock Proteins); 0 (RNA, Messenger)
[Em] Mês de entrada:1712
[Cu] Atualização por classe:171220
[Lr] Data última revisão:
171220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170430
[St] Status:MEDLINE


  5 / 1106 MEDLINE  
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[PMID]:28457919
[Au] Autor:Ma L; Su L; Liu H; Zhao F; Zhou D; Duan D
[Ad] Endereço:Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China; Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy o
[Ti] Título:Norovirus contamination and the glycosphingolipid biosynthesis pathway in Pacific oyster: A transcriptomics study.
[So] Source:Fish Shellfish Immunol;66:26-34, 2017 Jul.
[Is] ISSN:1095-9947
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Noroviruses are the primary pathogens associated with shellfish-borne gastroenteritis outbreaks. These viruses remain stable in oysters, suggesting an active mechanism for virus concentration. In this study, a deep RNA sequencing technique was used to analyze the transcriptome profiles of Pacific oysters at different time points after inoculation with norovirus (GII.4). We obtained a maximum of 65, 294, 698 clean sample reads. When aligned to the reference genome, the average mapping ratio of clean data was approximately 65%. In the samples harvested at 12, 24, and 48 h after contamination, 2,223, 2,990, and 2020 genes, respectively, were differentially expressed in contaminated and non-contaminated oyster digestive tissues, including 500, 1748, and 1039 up-regulated and 1723, 1242, and 981 down-regulated genes, respectively. In particular, FUT2 and B3GNT4, genes encoding the signaling components of glycosphingolipid biosynthesis, were significantly up-regulated in contaminated samples. In addition, we found up-regulation of some immune- and disease-related genes in the MHC I pathway (PA28, HSP 70, HSP90, CANX, BRp57, and CALR) and MHC II pathway (GILT, CTSBLS, RFX, and NFY), although NoVs did not cause diseases in the oysters. We detected two types of HBGA-like molecules with positive-to-negative ratios similar to type A and H1 HBGA-like molecules in digestive tissues that were significantly higher in norovirus-contaminated than in non-contaminated oysters. Thus, our transcriptome data analysis indicated that a human pathogen (GII.4 Norovirus) was likely concentrated in the digestive tissues of oysters via HBGA-like molecules that were synthesized by the glycosphingolipid biosynthesis pathway. The identified differentially expressed genes also provide potential candidates for functional analysis to identify genes involved in the accumulation of noroviruses in oysters.
[Mh] Termos MeSH primário: Crassostrea/metabolismo
Crassostrea/virologia
Glicoesfingolipídeos/metabolismo
Norovirus/fisiologia
Transcriptoma
Regulação para Cima
[Mh] Termos MeSH secundário: Animais
Vias Biossintéticas
Análise de Sequência de RNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Glycosphingolipids)
[Em] Mês de entrada:1712
[Cu] Atualização por classe:171212
[Lr] Data última revisão:
171212
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170502
[St] Status:MEDLINE


  6 / 1106 MEDLINE  
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[PMID]:29020114
[Au] Autor:Payton L; Sow M; Massabuau JC; Ciret P; Tran D
[Ad] Endereço:University of Bordeaux, EPOC, UMR 5805, Arcachon, France.
[Ti] Título:How annual course of photoperiod shapes seasonal behavior of diploid and triploid oysters, Crassostrea gigas.
[So] Source:PLoS One;12(10):e0185918, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:In this work, we study if ploidy (i.e. number of copies of chromosomes) in the oyster Crassostrea gigas may introduce differences in behavior and in its synchronization by the annual photoperiod. To answer to the question about the effect of the seasonal course of the photoperiod on the behavior of C. gigas according to its ploidy, we quantified valve activity by HFNI valvometry in situ for 1 year in both diploid and triploid oysters. Chronobiological analyses of daily, tidal and lunar rhythms were performed according the annual change of the photoperiod. In parallel, growth and gametogenesis status were measured and spawning events were detected by valvometry. The results showed that triploids had reduced gametogenesis, without spawning events, and approximately three times more growth than diploids. These differences in physiological efforts could explain the result that photoperiod (daylength and/or direction of daylength) differentially drives and modulates seasonal behavior of diploid and triploid oysters. Most differences were observed during long days (spring and summer), where triploids showed longer valve opening duration but lower opening amplitude, stronger daily rhythm and weaker tidal rhythm. During this period, diploids did major gametogenesis and spawning whereas triploids did maximal growth. Differences were also observed in terms of moonlight rhythmicity and neap-spring tidal cycle rhythmicity. We suggest that the seasonal change of photoperiod differentially synchronizes oyster behavior and biological rhythms according to physiological needs based on ploidy.
[Mh] Termos MeSH primário: Comportamento Animal/fisiologia
Crassostrea/genética
Diploide
Fotoperíodo
Estações do Ano
Triploidia
[Mh] Termos MeSH secundário: Animais
Ritmo Circadiano
Crassostrea/crescimento & desenvolvimento
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171031
[Lr] Data última revisão:
171031
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171012
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0185918


  7 / 1106 MEDLINE  
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[PMID]:28945769
[Au] Autor:Song K; Li L; Zhang G
[Ad] Endereço:Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China.
[Ti] Título:The association between DNA methylation and exon expression in the Pacific oyster Crassostrea gigas.
[So] Source:PLoS One;12(9):e0185224, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: DNA methylation is one of the most important epigenetic modifications of eukaryotic genomes and is believed to play integral roles in diverse biological processes. Although DNA methylation has been well studied in mammals, data are limited in invertebrates, particularly Mollusca. The Pacific oyster Crassostrea gigas is an emerging genetic model for functional analysis of DNA methylation in Mollusca. Recent studies have shown that there is a positive association between methylation status and gene expression in C. gigas; however, whether this association exists at the exon level remains to be determined. RESULTS: In this study, we characterized the genome-wide methylation pattern across two different tissues of C. gigas and found that methylated genes are expressed in more tissues and development stages than unmethylated genes. Furthermore, we found that different types of exons had different methylation levels, with the lowest methylation levels in the first exons, followed by the last exons, and the internal exons. We found that the exons included in the gene transcript contained significantly higher DNA methylation levels than skipped exons. We observed that the DNA methylation levels increased slowly after the start sites and end sites of exons seperately, and then decreased quickly towards the middle sites of exons. We also found that methylated exons were significantly longer than unmethylated exons. CONCLUSION: This study constitutes the first genome-wide analysis to show an association between exon-level DNA methylation and mRNA expression in the oyster. Our findings suggest that exon-level DNA methylation may play a role in the construction of alternative splicing by positively influencing exon inclusion during transcription.
[Mh] Termos MeSH primário: Crassostrea/genética
Metilação de DNA
[Mh] Termos MeSH secundário: Animais
Ilhas de CpG
Epigênese Genética
Éxons
Expressão Gênica
Perfilação da Expressão Gênica
Masculino
Modelos Genéticos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171023
[Lr] Data última revisão:
171023
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170926
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0185224


  8 / 1106 MEDLINE  
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[PMID]:28934317
[Au] Autor:Barillé L; Le Bris A; Méléder V; Launeau P; Robin M; Louvrou I; Ribeiro L
[Ad] Endereço:Laboratoire Mer Molécules Santé (EA2160), Institut Universitaire Mer et Littoral (FR_C 3473), Université de Nantes, Nantes, France.
[Ti] Título:Photosynthetic epibionts and endobionts of Pacific oyster shells from oyster reefs in rocky versus mudflat shores.
[So] Source:PLoS One;12(9):e0185187, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The Pacific oyster, Crassostrea gigas (Thunberg), is the main bivalve species cultivated in the world. With global warming enabling its reproduction and larval survival at higher latitudes, this species is now recognized as invasive and creates wild oyster reefs globally. In this study, the spatial distribution of photosynthetic assemblages colonizing the shells of wild C. gigas was investigated on both a large scale (two contrasting types of reefs found in mudflats and rocky areas) and a small scale (within individual shells) using a hyperspectral imager. The microspatial distribution of all phototrophs was obtained by mapping the Normalized Difference Vegetation Index (NDVI). Second derivative (δδ) analyses of hyperspectral images at 462, 524, 571 and 647 nm were subsequently applied to map diatoms, cyanobacteria, rhodophytes and chlorophytes, respectively. A concomitant pigment analysis was carried out by high performance liquid chromatography and completed by taxonomic observations. This study showed that there was high microalgal diversity associated with wild oyster shells and that there were differences in the structure of the phototropic assemblages depending on the type of reef. Namely, vertically-growing oysters in mudflat areas had a higher biomass of epizoic diatoms (hyperspectral proxy at δδ462 nm) and were mainly colonized by species of the genera Navicula, Nitzschia and Hippodonta, which are epipelic or motile epipsammic. The assemblages on the horizontal oysters contained more tychoplanktonic diatoms (e.g. Thalassiosira pseudonana, T. proschkinae and Plagiogrammopsis vanheurckii). Three species of boring cyanobacteria were observed for both types of reef: Mastigocoleus testarum, Leptolyngbya terrebrans, and Hyella caespistosa, but the second derivative analysis at 524 nm showed a significantly higher biomass for the horizontally-growing oysters. There was no biomass difference for the boring chlorophyte assemblages (δδ647 nm), with two species: Eugomontia testarum and Ostreobium quekettii observed for both types of reef. This study shows that oyster shells are an idiosyncratic but ubiquitous habitat for phototrophic assemblages. The contribution of these assemblages in terms of biomass and production to the functioning of coastal areas, and particularly to shellfish ecosystems, remains to be evaluated.
[Mh] Termos MeSH primário: Crassostrea/fisiologia
Fotossíntese
Simbiose
[Mh] Termos MeSH secundário: Animais
Biodiversidade
Biomassa
Pigmentação
Plantas/classificação
Plantas/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171024
[Lr] Data última revisão:
171024
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170922
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0185187


  9 / 1106 MEDLINE  
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[PMID]:28934286
[Au] Autor:Arfken A; Song B; Bowman JS; Piehler M
[Ad] Endereço:Department of Biological Sciences, Virginia Institute of Marine Science, Gloucester Point, Virginia, United States of America.
[Ti] Título:Denitrification potential of the eastern oyster microbiome using a 16S rRNA gene based metabolic inference approach.
[So] Source:PLoS One;12(9):e0185071, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The eastern oyster (Crassostrea virginica) is a foundation species providing significant ecosystem services. However, the roles of oyster microbiomes have not been integrated into any of the services, particularly nitrogen removal through denitrification. We investigated the composition and denitrification potential of oyster microbiomes with an approach that combined 16S rRNA gene analysis, metabolic inference, qPCR of the nitrous oxide reductase gene (nosZ), and N2 flux measurements. Microbiomes of the oyster digestive gland, the oyster shell, and sediments adjacent to the oyster reef were examined based on next generation sequencing (NGS) of 16S rRNA gene amplicons. Denitrification potentials of the microbiomes were determined by metabolic inferences using a customized denitrification gene and genome database with the paprica (PAthway PRediction by phylogenetIC plAcement) bioinformatics pipeline. Denitrification genes examined included nitrite reductase (nirS and nirK) and nitrous oxide reductase (nosZ), which was further subdivided by genotype into clade I (nosZI) or clade II (nosZII). Continuous flow through experiments measuring N2 fluxes were conducted with the oysters, shells, and sediments to compare denitrification activities. Paprica properly classified the composition of microbiomes, showing similar classification results from Silva, Greengenes and RDP databases. Microbiomes of the oyster digestive glands and shells were quite different from each other and from the sediments. The relative abundance of denitrifying bacteria inferred by paprica was higher in oysters and shells than in sediments suggesting that oysters act as hotspots for denitrification in the marine environment. Similarly, the inferred nosZI gene abundances were also higher in the oyster and shell microbiomes than in the sediment microbiome. Gene abundances for nosZI were verified with qPCR of nosZI genes, which showed a significant positive correlation (F1,7 = 14.7, p = 6.0x10-3, R2 = 0.68). N2 flux rates were significantly higher in the oyster (364.4 ± 23.5 µmol N-N2 m-2 h-1) and oyster shell (355.3 ± 6.4 µmol N-N2 m-2 h-1) compared to the sediment (270.5 ± 20.1 µmol N-N2 m-2 h-1). Thus, bacteria carrying nosZI genes were found to be an important denitrifier, facilitating nitrogen removal in oyster reefs. In addition, this is the first study to validate the use of 16S gene based metabolic inference as a method for determining microbiome function, such as denitrification, by comparing inference results with qPCR gene quantification and rate measurements.
[Mh] Termos MeSH primário: Crassostrea/metabolismo
Crassostrea/microbiologia
Desnitrificação/fisiologia
Microbiota/fisiologia
[Mh] Termos MeSH secundário: Exoesqueleto/metabolismo
Exoesqueleto/microbiologia
Animais
Biologia Computacional
Sistema Digestório/metabolismo
Sistema Digestório/microbiologia
Modelos Lineares
Microbiota/genética
Nitrogênio/metabolismo
North Carolina
Oceanos e Mares
Reação em Cadeia da Polimerase
RNA Ribossômico 16S/genética
Rios
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Ribosomal, 16S); N762921K75 (Nitrogen)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171024
[Lr] Data última revisão:
171024
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170922
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0185071


  10 / 1106 MEDLINE  
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[PMID]:28901906
[Au] Autor:Baek C; Kim E; Shin SK; Choi S; Yi H
[Ad] Endereço:1​Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea.
[Ti] Título:Hydrogenophaga crassostreae sp. nov., isolated from a Pacific oyster.
[So] Source:Int J Syst Evol Microbiol;67(10):4045-4049, 2017 Oct.
[Is] ISSN:1466-5034
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:A Gram-negative, motile, rod-shaped, and aerobic bacterial strain, designated LPB0072 , was isolated from a Pacific oyster (Crassostrea gigas). Autotrophic growth with hydrogen gas was not observed. Cells oxidized thiosulfate to sulfate and reduced nitrate to nitrite. The complete genome sequence of strain LPB0072 (CP017476) is 4.94 Mb in length and contains 4459 protein-coding genes, with a G+C content of 61.3 mol%. Analysis of the 16S rRNA gene sequence indicated that strain LPB0072 belongs to the genus Hydrogenophaga, with greatest sequence similarity to the type strain of Hydrogenophaga taeniospiralis (97.5 %). The isoprenoid quinone (Q-8) and the major cellular fatty acids (C16 : 1ω7c and/or C16 : 1ω6c, C16 : 0 and C17 : 1ω6c) identified were concordant with the chemotaxonomic properties of the genus Hydrogenophaga. The average nucleotide identities with closely related species were below the suggested boundary for species delineation, indicating that the isolate is a novel species. Numerous physiological and biochemical features also distinguished the isolate from other known Hydrogenophaga species. Based on the polyphasic data presented in this study, strain LPB0072 should be classified as a novel species in the genus Hydrogenophaga, and the name Hydrogenophaga crassostreae sp. nov. is proposed. The type strain is LPB0072 (=KACC 18705 =JCM 31188 ).
[Mh] Termos MeSH primário: Comamonadaceae/classificação
Crassostrea/microbiologia
Filogenia
[Mh] Termos MeSH secundário: Animais
Técnicas de Tipagem Bacteriana
Composição de Bases
Comamonadaceae/genética
Comamonadaceae/isolamento & purificação
DNA Bacteriano/genética
Ácidos Graxos/química
Oceano Pacífico
RNA Ribossômico 16S/genética
Análise de Sequência de DNA
Ubiquinona/química
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Bacterial); 0 (Fatty Acids); 0 (RNA, Ribosomal, 16S); 1339-63-5 (Ubiquinone); CQA993F7P8 (ubiquinone 8)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171101
[Lr] Data última revisão:
171101
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170914
[St] Status:MEDLINE
[do] DOI:10.1099/ijsem.0.002244



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