Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 121
Filtrar
Mais filtros










Tipo de estudo
Intervalo de ano de publicação
1.
Int J Syst Evol Microbiol ; 70(4): 2682-2689, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32141810

RESUMO

Three aerobic, rod-shaped actinobacterial strains, designated MMS17-SY117T, MMS17-SY207-3T and MMS17-SY213T, were isolated from soil and their taxonomic positions were analysed using a polyphasic approach. The isolates showed best growth at 30 °C, pH 7 and 0-1 % (w/v) NaCl. On the basis of 16S rRNA gene sequence similarity, the isolates were affiliated to the genus Nocardioides, and the closest species to MMS17-SY117T, MMS17-SY207-3T and MMS17-SY213T were Nocardioides aestuarii JC2056T (97.76%), Nocardioides currus IB-3T (97.41%) and Nocardioides exalbidus RC825T (98.71%), respectively. Each isolate formed a distinct cluster within the Nocardioides clade in the phylogenetic tree. The orthologous average nucleotide identity and digital DNA-DNA hybridization values were in the range of 74.4-85.7 % and 16.6-39.2 %, respectively, with the type strains of related species. The major polar lipids in all three strains were phosphatidylinositol, phosphatidylglycerol and diphosphatidylglycerol. The predominant fatty acids were iso-C16 : 0 and C17 : 1 ω8c. MK-8(H4) was the major isoprenoid quinone and ll-DAP was the major diamino acid. Galactose, glucose and rhamnose were present in the whole-cell hydrolysate, and MMS17-SY213T also contained mannose and ribose. The DNA G+C contents of MMS17-SY117T, MMS17-SY207-3T and MMS17-SY213T were 72.2, 70.4 and 71.5 mol%, respectively. The phylogenetic, phenotypic and chemotaxonomic data supported the classification of each strain as representing a new species of Nocardioides, for which the names Nocardioides euryhalodurans sp. nov. (MMS17-SY117T=KCTC 49175T=JCM 32831T), Nocardioides seonyuensis sp. nov. (MMS17-SY207-3T=KCTC 49176T=JCM 32832T) and Nocardioides eburneiflavus sp. nov. (MMS17-SY213T=KCTC 49177T=JCM 32833T) are proposed accordingly.


Assuntos
Actinobacteria/classificação , Filogenia , Microbiologia do Solo , Actinobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Areia/microbiologia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
2.
BMC Genomics ; 21(1): 118, 2020 Feb 03.
Artigo em Inglês | MEDLINE | ID: mdl-32013859

RESUMO

BACKGROUND: Acidophilic members of the genus Streptomyces can be a good source for novel secondary metabolites and degradative enzymes of biopolymers. In this study, a genome-based approach on Streptomyces yeochonensis CN732, a representative neutrotolerant acidophilic streptomycete, was employed to examine the biosynthetic as well as enzymatic potential, and also presence of any genetic tools for adaptation in acidic environment. RESULTS: A high quality draft genome (7.8 Mb) of S. yeochonensis CN732 was obtained with a G + C content of 73.53% and 6549 protein coding genes. The in silico analysis predicted presence of multiple biosynthetic gene clusters (BGCs), which showed similarity with those for antimicrobial, anticancer or antiparasitic compounds. However, the low levels of similarity with known BGCs for most cases suggested novelty of the metabolites from those predicted gene clusters. The production of various novel metabolites was also confirmed from the combined high performance liquid chromatography-mass spectrometry analysis. Through comparative genome analysis with related Streptomyces species, genes specific to strain CN732 and also those specific to neutrotolerant acidophilic species could be identified, which showed that genes for metabolism in diverse environment were enriched among acidophilic species. In addition, the presence of strain specific genes for carbohydrate active enzymes (CAZyme) along with many other singletons indicated uniqueness of the genetic makeup of strain CN732. The presence of cysteine transpeptidases (sortases) among the BGCs was also observed from this study, which implies their putative roles in the biosynthesis of secondary metabolites. CONCLUSIONS: This study highlights the bioactive potential of strain CN732, an acidophilic streptomycete with regard to secondary metabolite production and biodegradation potential using genomics based approach. The comparative genome analysis revealed genes specific to CN732 and also those among acidophilic species, which could give some insights into the adaptation of microbial life in acidic environment.

3.
Int J Syst Evol Microbiol ; 70(3): 2079-2083, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31995467

RESUMO

A mycolic acid-containing actinobacterium designated strain MMS17-SY073T was isolated from island soil. The isolate showed best growth at 25 °C, pH 6, and 0 % (w/v) NaCl. The phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MMS17-SY073T belongs to the genus Gordonia, and is mostly related to the type strains of Gordonia soli (98.5 % sequence similarity), Gordonia polyisoprenivorans (98.1%), and Gordonia hankookensis (97.8%). The genome-based comparisons showed a clear distinction between the strain and the two neighbouring species, G. soli and G. polyisoprenivorans, with the average nucleotide identities (ANI) of 75.8 and 76.3 %, respectively. Notably, the genome of strain MMS17-SY073T was the largest in total stretch and gene counts among the complete genomes of Gordonia, and contained a number of biosynthetic gene clusters for secondary metabolites, in particular those for non-ribosomal peptide synthetases. The major polar lipids were diphosphatidyl glycerol (DPG), phosphatidyl glycerol (PG), phosphatidyl ethanolamine (PE), phosphatidyl inositol (PI) and phosphatidyl inositol mannoside (PIM). The isoprenoid quinone was MK-9(H2), and the main fatty acids were C16 : 0 (30.2%) and 10-methyl-C18 : 0 (33.7%). The whole cell hydrolysates contained galactose, arabinose, and meso-diaminopimelic acid. The DNA G+C content was 67.4 mol%. Based on phenotypic, chemotaxonomic and genetic analysis, strain MMS17-SY073T should be classified as a new species of the genus Gordonia, for which the name Gordonia insulae sp. nov. is proposed (type strain=MMS17-SY073T=KCTC 49257T=JCM 33277T).


Assuntos
Gordonia (Bactéria)/classificação , Filogenia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Gordonia (Bactéria)/isolamento & purificação , Ilhas , Ácidos Micólicos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
4.
Gene ; 733: 144379, 2020 Apr 05.
Artigo em Inglês | MEDLINE | ID: mdl-31972312

RESUMO

An actinobacterial strain designated Kitasatospora sp. MMS16-BH015, exhibiting high level of heavy metal resistance, was isolated from soil of an abandoned metal mining site, and its potential for metal resistance and secondary metabolite production was studied. The strain was resistant to multiple heavy metals including zinc (up to 100 mM), nickel (up to 2 mM) and copper (up to 0.8 mM), and also showed antimicrobial potential against a broad group of microorganisms, in particular filamentous fungi. The genome of strain MMS16-BH015 was 8.96 Mbp in size with a G + C content of 72.7%, and contained 7270 protein-coding genes and 107 tRNA/rRNA genes. The genome analysis revealed presence of at least 121 metal resistance related genes, which was prominently higher in strain MMS16-BH015 compared to other genomes of Kitasatospora. The genes included those for proteins representing various families involved in the transport of heavy metals, for example dipeptide transport ATP-binding proteins, high-affinity nickel transport proteins, and P-type heavy metal-transporting ATPases. Additionally, 43 biosynthetic gene clusters (BGCs) for secondary metabolites, enriched with those for non-ribosomal peptides, were detected in this multiple heavy metal resistant actinobacterium, which was again the highest among the compared genomes of Kitasatospora. The pan-genome analysis also identified higher numbers of unique genes related to secondary metabolite production and metal resistance mechanism in strain MMS16-BH015. A high level of correlation between the biosynthetic potential and heavy metal resistance could be observed, thus indicating that heavy metal resistant actinobacteria can be a promising source of bioactive compounds.


Assuntos
Actinobacteria/efeitos dos fármacos , Actinobacteria/genética , Antibacterianos/farmacologia , Proteínas de Bactérias/genética , Farmacorresistência Bacteriana/genética , Genoma Bacteriano , Metais Pesados/farmacologia , Actinobacteria/classificação , Actinobacteria/isolamento & purificação , Mineração , Família Multigênica , Filogenia , Microbiologia do Solo
5.
Int J Syst Evol Microbiol ; 69(5): 1350-1354, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30896386

RESUMO

A novel actinobacterial strain producing an antifungal substance was isolated from a sample of acidic mine area soil, and its taxonomic position was evaluated. The novel strain, designated TW1S1T, formed white-grey aerial mycelium and yellow substrate mycelium on oatmeal agar. Growth occurred at 10-45 °C (optimum, 30 °C), pH 4-9 (pH 6-7) and in the presence of up to 8 % (w/v) NaCl. Melanin was produced on peptone-yeast extract-iron agar. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that the novel strain should be assigned to the genus Streptomyces, and the closest species was Streptomyces puniciscabiei S77T with 99.1 % sequence similarity, which was followed by Streptomyces durhamensis NRRL B-3309T (99.0 %), Streptomyces filipinensis NBRC 12860T (98.9 %) and Streptomyces yaanensis Z4T (98.7 %). The chemotaxonomic properties were consistent with those of Streptomyces. ll-Diaminopimelic acid was the diagnostic diamino acid, and alanine, glutamic acid and glycine were present in the peptidoglycan. The cell-wall hydrolysate also contained galactose, glucose, mannose and ribose. The predominant isoprenoid quinones were MK-9(H4) and MK-9(H6), the major polar lipids were phosphatidylglycerol and an unidentified phospholipid, and the main fatty acids were iso-C16 : 0 and anteiso-C15 : 0. However, strain TW1S1T could be distinguished from its neighbouring species by its phenotypic properties. In addition, the genome-based comparison with the closest species indicated that strain TW1S1T should be recognized as a separate species. The phylogenetic, phenotypic and chemotaxonomic as well as genomic evidence supported that TW1S1T represents a novel species of Streptomyces, for which the name Streptomycesfodineus sp. nov. is proposed (type strain, TW1S1T = KCTC 49013T = JCM 32404T).


Assuntos
Mineração , Filogenia , Microbiologia do Solo , Streptomyces/classificação , Antibiose , Antifúngicos , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Peptidoglicano/química , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Streptomyces/isolamento & purificação , Vitamina K 2/análogos & derivados , Vitamina K 2/química
6.
J Microbiol ; 57(6): 431-443, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30900148

RESUMO

Sortases are cysteine transpeptidases that assemble surface proteins and pili in their cell envelope. Encoded by all Gram-positive bacteria, few Gram-negative bacteria and archaea, sortases are currently divided into six classes (A-F). Due to the steep increase in bacterial genome data in recent years, the number of sortase homologues have also escalated rapidly. In this study, we used protein sequence similarity networks to explore the taxonomic diversity of sortases and also to evaluate the current classification of these enzymes. The resultant data suggest that sortase classes A, B, and D predominate in Firmicutes and classes E and F are enriched in Actinobacteria, whereas class C is distributed in both Firmicutes and Actinobacteria except Streptomyces family. Sortases were also observed in various Gram-negatives and euryarchaeota, which should be recognized as novel classes of sortases. Motif analysis around the catalytic cysteine was also performed and suggested that the residue at 2nd position from cysteine may help distinguish various sortase classes. Moreover, the sequence analysis indicated that the catalytic arginine is highly conserved in almost all classes except sortase F in which arginine is replaced by asparagine in Actinobacteria. Additionally, class A sortases showed higher structural variation as compared to other sortases, whereas inter-class comparisons suggested structures of class C and D2 exhibited best similarities. A better understanding of the residues highlighted in this study should be helpful in elucidating their roles in substrate binding and the sortase function, and successively could help in the development of strong sortase inhibitors.


Assuntos
Aminoaciltransferases/química , Aminoaciltransferases/classificação , Proteínas de Bactérias/química , Proteínas de Bactérias/classificação , Cisteína Endopeptidases/química , Cisteína Endopeptidases/classificação , Actinobacteria/metabolismo , Sequência de Aminoácidos , Aminoaciltransferases/genética , Aminoaciltransferases/fisiologia , Archaea/metabolismo , Bactérias/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/fisiologia , Simulação por Computador , Cisteína/metabolismo , Cisteína Endopeptidases/genética , Cisteína Endopeptidases/fisiologia , Fímbrias Bacterianas , Genoma Bacteriano , Proteínas de Membrana , Modelos Moleculares , Filogenia , Domínios e Motivos de Interação entre Proteínas , Alinhamento de Sequência , Análise de Sequência
7.
J Microbiol ; 57(5): 356-361, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30796748

RESUMO

A Gram-stain-negative, mucus-forming, motile by gliding, non-spore-forming and short rod-shaped bacterial strain designated R1-15T was isolated from soil and its taxonomic position was evaluated using a polyphasic approach. Strain R1-15T grew at 15-37°C (optimum, 30°C), at pH 6-7 (optimum, pH 6) and in the presence of 0-1% (w/v) NaCl (optimum, 0%) on 0.1X TSA. On the basis of 16S rRNA gene sequence similarity, the novel strain was assigned to the family Chitinophagaceae of the phylum Bacteroidetes, and its closest related taxa were species of the genera Taibaiella (88.76-90.02% sequence similarity), Lacibacter (89.24-90.00%), Chitinophaga (88.61-89.76%), and Terrimonas (89.04%). Flexirubin- type pigments were produced. The only isoprenoid quinone was MK-7, and the major polar lipid was phosphatidylethanolamine. Based on whole genome comparisons between the strain R1-15T and the type strains of relatives, the orthologous average nucleotide identity values were 66.9-67.0%. The DNA G + C content of strain R1-15T was 43.8 mol%. The combination of phylogenetic, chemotaxonomic and phenotypic data clearly supported separation of strain R1-15T from related taxa, and thus the name Mucibacter soli gen. nov., sp. nov. is proposed. The type strain is R1-15T (= KCTC 62274T = JCM 31190T).


Assuntos
Bacteroidetes , Mucinas/biossíntese , Técnicas de Tipagem Bacteriana , Bacteroidetes/classificação , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Bacteroidetes/metabolismo , Composição de Bases/genética , DNA Bacteriano/genética , Locomoção/fisiologia , Fosfatidiletanolaminas/metabolismo , RNA Ribossômico 16S/genética , Microbiologia do Solo
8.
J Nat Prod ; 82(2): 341-348, 2019 02 22.
Artigo em Inglês | MEDLINE | ID: mdl-30735389

RESUMO

Five new tripeptides, acidiphilamides A-E (1-5), were discovered along with two previously reported compounds, l-isoleucinamide (6) and l-valinamide (7), from Streptacidiphilus rugosus AM-16, an acidophilic actinobacterial strain isolated from acidic forest soil. The structures of 1-5 were elucidated as modified tripeptides bearing phenylalaninol or methioninol fragments with C3-C5 acyl chains based mainly on NMR and mass spectroscopic data. The absolute configurations of the amine units were established by advanced Marfey's method and GITC (2,3,4,6-tetra- O-acetyl-ß-d-glucopyranosyl isothiocyanate) derivatization followed by LC/MS analysis. Acidiphilamides A and B (1 and 2), the first secondary metabolites isolated from the rare actinobacterial genus Streptacidiphilus, significantly inhibited autophagic flux but not proteasome activity in HeLa cells. These compounds appeared to block mainly the autophagosome-lysosome fusion step in the late stage of cellular autophagy.


Assuntos
Actinobacteria/metabolismo , Autofagia/efeitos dos fármacos , Oligopeptídeos/isolamento & purificação , Células HeLa , Humanos , Oligopeptídeos/química , Oligopeptídeos/farmacologia
9.
Gut Liver ; 13(1): 93-103, 2019 01 15.
Artigo em Inglês | MEDLINE | ID: mdl-30400723

RESUMO

Background/Aims: To investigate the treatment efficacy and renal safety of long-term tenofovir disoproxil fumarate (TDF) therapy in chronic hepatitis B (CHB) patients with preserved renal function. Methods: The medical records of 919 CHB patients who were treated with TDF therapy were reviewed. All patients had preserved renal function with an estimated glomerular filtration rate (eGFR) of at least 60 mL/min/1.73 m². Results: A total of 426 patients (184 treatment-naïve and 242 treatment-experienced) were included for analysis. A virologic response (VR) was defined as achieving an undetectable serum hepatitis B virus (HBV) DNA level, and the overall VR was 74.9%, 86.7%, and 89.4% at the 1, 2, and 3-year follow-ups, respectively. Achieving a VR was not influenced by previous treatment experience, TDF combination therapy, or antiviral resistance. In a multivariate analysis, being hepatitis B e antigen positive at baseline and having a serum HBV DNA level ≥2,000 IU/mL at 12 months were associated with lower VR rates during the long-term TDF therapy. The overall renal impairment was 2.9%, 1.8%, and 1.7% at the 1, 2, and 3-year follow-ups, respectively. With regard to renal safety, underlying diabetes mellitus (DM) and an initial eGFR of 60 to 89 mL/min/1.73 m² were significant independent predictors of renal impairment. Conclusions: TDF therapy appears to be an effective treatment option for CHB patients with a preserved GFR. However, patients with underlying DM and initial mild renal dysfunction (eGFR, 60 to 89 mL/min/1.73 m²) have an increased risk of renal impairment.


Assuntos
Adenina/análogos & derivados , Antivirais/administração & dosagem , Taxa de Filtração Glomerular/efeitos dos fármacos , Vírus da Hepatite B/efeitos dos fármacos , Hepatite B Crônica/tratamento farmacológico , Ácidos Fosforosos/administração & dosagem , Adenina/administração & dosagem , Adenina/efeitos adversos , Adulto , Antivirais/efeitos adversos , Esquema de Medicação , Feminino , Hepatite B Crônica/fisiopatologia , Hepatite B Crônica/virologia , Humanos , Rim/efeitos dos fármacos , Rim/fisiopatologia , Rim/virologia , Nefropatias/induzido quimicamente , Nefropatias/epidemiologia , Nefropatias/virologia , Masculino , Pessoa de Meia-Idade , Análise Multivariada , Ácidos Fosforosos/efeitos adversos , Estudos Retrospectivos , Fatores de Tempo , Resultado do Tratamento
10.
Int J Syst Evol Microbiol ; 68(9): 3149-3155, 2018 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-30102143

RESUMO

A moderately acidophilic actinobacterial strain, designated MMS16-CNU450T, was isolated from pine grove soil, and its taxonomic position was analysed using a polyphasic approach. The isolate showed best growth at 30 °C, pH 6 and 0.5 % (w/v) NaCl. On the basis of 16S rRNA gene sequence similarity, the isolate was assigned to the genus Streptacidiphilus, and the closest species were Streptacidiphilus rugosus AM-16T (sequence similarity, 98.61 %), Streptacidiphilus melanogenes NBRC 103184T (98.53 %), Streptacidiphilus jiangxiensis NBRC 100920T (98.19 %) and Streptacidiphilus anmyonensis NBRC 103185T (98.05 %). The isolate formed a distinct cluster of its own within the Streptacidiphilusclade in the phylogenetic tree. Based on whole-genome comparison between the strain MMS16-CNU450T and the type strains of related species, the orthologous average nucleotide identity and in silico DNA-DNA hybridization values were in the range of 77.9-87.0 and 22.3-32.7 %, respectively. The DNA G+C content of the isolate was 68.6 mol%. The phylogenetic, phenotypic, chemotaxonomic and genomic data supported the affiliation of the strain to Streptacidiphilus, and the name Streptacidiphilus pinicola sp. nov. (type strain, MMS16-CNU450T=KCTC 49008T=JCM 32300T) is proposed accordingly.


Assuntos
Florestas , Filogenia , Pinus/microbiologia , Microbiologia do Solo , Streptomycetaceae/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Streptomycetaceae/genética , Streptomycetaceae/isolamento & purificação
11.
Int J Syst Evol Microbiol ; 68(9): 2960-2966, 2018 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-30028285

RESUMO

Three Gram-negative, non-spore-forming, rod-shaped and motile bacterial strains, designated MMS16-UL250T, MMS16-UL253T and MMS16-UL482T, were isolated from coastal seawater and subjected to taxonomic characterization. All isolates grew at 4-30 °C (optimum, 25 °C), at pH 6-10 (pH 7) and in the presence of up to 8 % NaCl (2.5-4.5 %). The 16S rRNA gene sequence similarities between the three isolates and Shewanella algicola St-6T, the closest species, were 98.1-99.2 %, and those among the isolates were 98.5-99.0 %. In the phylogenetic tree, MMS16-UL250T formed a cluster with S. algicola St-6T, but the DNA-DNA relatedness between the two strains was 28.8±1.5 %, thus confirming their separation at species level. The other two strains formed separate phylogenetic lines respectively. The main quinones for all strains were Q-7, Q-8, MK-7 and MMK-7, which is typical for Shewanella. The major polar lipids of all strains were phosphatidylglycerol and phosphatidylethanolamine, and the common major fatty acid was a summed feature consisting of C16 : 1ω7c and/or C16 : 1ω6c while the proportions varied among the three strains. The DNA G+C contents of the strains also varied between 42.1 and 43.7 mol%. Phenotypic properties distinguished each strain from S. algicola as well as from one another. Based on the polyphasic analysis, each strain is considered to represent a novel species of Shewanella, for which the names Shewanellasaliphila sp. nov. (type strain, MMS16-UL250T=KCTC 62131T=JCM 32304T), Shewanella ulleungensis sp. nov. (type strain, MMS16-UL253T=KCTC 62130T=JCM 32305T) and Shewanella litoralis sp. nov. (type strain, MMS16-UL482T=KCTC 62129T=JCM 32306T) are proposed.


Assuntos
Filogenia , Água do Mar/microbiologia , Shewanella/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Shewanella/genética , Shewanella/isolamento & purificação , Vitamina K 2/análogos & derivados , Vitamina K 2/química
12.
Remote Sens Environ ; 213: 1-17, 2018 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-30050230

RESUMO

A method to assess global land surface water (fw) inundation dynamics was developed by exploiting the enhanced fw sensitivity of L-band (1.4 GHz) passive microwave observations from the Soil Moisture Active Passive (SMAP) mission. The L-band fw (fwLBand ) retrievals were derived using SMAP H-polarization brightness temperature (Tb ) observations and predefined L-band reference microwave emissivities for water and land endmembers. Potential soil moisture and vegetation contributions to the microwave signal were represented from overlapping higher frequency Tb observations from AMSR2. The resulting fwLBand global record has high temporal sampling (1-3 days) and 36-km spatial resolution. The fwLBand annual averages corresponded favourably (R=0.85, p-value<0.001) with a 250-m resolution static global water map (MOD44W) aggregated at the same spatial scale, while capturing significant inundation variations worldwide. The monthly fwLBand averages also showed seasonal inundation changes consistent with river discharge records within six major US river basins. An uncertainty analysis indicated generally reliable fwLBand performance for major land cover areas and under low to moderate vegetation cover, but with lower accuracy for detecting water bodies covered by dense vegetation. Finer resolution (30-m) fwLBand results were obtained for three sub-regions in North America using an empirical downscaling approach and ancillary global Water Occurrence Dataset (WOD) derived from the historical Landsat record. The resulting 30-m fwLBand retrievals showed favourable spatial accuracy for water (commission error 31.46%, omission error 30.20%) and land (commission error 0.87%, omission error 0.96%) classifications and seasonal wet and dry periods when compared to independent water maps derived from Landsat-8 imagery. The new fwLBand algorithms and continuing SMAP and AMSR2 operations provide for near real-time, multi-scale monitoring of global surface water inundation dynamics and potential flood risk.

13.
Int J Syst Evol Microbiol ; 68(1): 165-169, 2018 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-29125459

RESUMO

A Gram-stain-positive strain, designated DT7-02T, was isolated from the surface-sterilized root of Oenotherabiennis (evening primrose) and subjected to taxonomic characterization. Cells of DT7-02T were slender rod-shaped, motile by means of flagella, and oxidase- and catalase-positive. The colonies were circular, pinkish-yellow, opaque, glistering and 1-2 mm in diameter. The strain was moderately thermophilic and halophilic, as growth occurred at 20-44 °C (optimum 40 °C), pH 7-10 (optimum pH 8-9) and in the presence of 0-8 % of NaCl (optimum 4 %) in tryptic soy broth. The analysis of 16S rRNA gene sequences indicated that the strain represented a member of the genus Pseudogracilibacillus of the family Bacillaceae, and the sequence similarity was 96.5 % with Pseudogracilibacillus auburnensis P-207T and 95.9 % with Pseudogracilibacillus marinus NIOT-bflm-S4T. Other related taxa were Ornithinibacillus contaminans DSM 22953T and Sinibacillus soli KCTC 33117T, with 16S rRNA gene sequence similarities of 95.4 and 94.3 %, respectively. The major cellular fatty acids of DT7-02T were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content was 35.1 mol%, and the respiratory quinone was MK-7. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The combination of chemotaxonomic properties enabled differentiation of DT7-02T from the other two species of the genus Pseudogracilibacillus. The results of phylogenetic, phenotypic and chemotaxonomic analyses demonstrate that strain DT7-02T (=KCTC 33854T=JCM 31192T) merits recognition as representing a novel species of the genus Pseudogracilibacillus, for which the name Pseudogracilibacillusendophyticus sp. nov. is proposed.


Assuntos
Oenothera biennis/microbiologia , Filogenia , Raízes de Plantas/microbiologia , Bacillaceae/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Peptidoglicano/química , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
14.
Int J Syst Evol Microbiol ; 68(1): 93-98, 2018 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-29111965

RESUMO

A Gram-stain-negative, yellow, facultatively-anaerobic, short, rod-shaped, non-spore-forming bacterium, designated PK15T, was isolated from freshwater. Growth was observed at 4-40 °C (optimum, 30 °C), pH 6-9 (optimum, 8), and in the presence of 0-0.8 % (w/v) NaCl (optimum, 0.4 %). Strain PK15T exhibited both catalase and oxidase activities and was able to reduce nitrate. On the basis of 16S rRNA gene sequence similarities, strain PK15T was shown to belong to the genus Flavobacterium with close similarities to Flavobacterium palustre S44T (97.9 %) and Flavobacterium seoulense EM1321T (97.7 %). Menaquinone-6 (MK-6) was the major respiratory quinone, while the G+C content of the genomic DNA was 35.5 (±0.9) mol%. The major polar lipids were phosphatidylethanolamine, three unidentified aminolipids, one unidentified aminophospholipid and three unidentified polar lipids. The predominant cellular fatty acids (≥10 %) were anteiso-C15 : 0 (17.3 %), a summed feature comprising C16 : 1ω7c and/or C16 : 1ω6c (15.1 %) and iso-C15 : 0 (10.0 %). Chemotaxonomic data supported the affiliation of strain PK15T to the genus Flavobacterium. The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain PK15T from strains of closely related species. It was, therefore, evident that PK15T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium commune sp. nov. is proposed with strain PK15T (=KCTC 52562T=JCM 32115T) as the type strain. Based on the results of the chemotaxonomic characterization in the present study, an emended description of Flavobacterium seoulense is also proposed.


Assuntos
Flavobacterium/classificação , Água Doce/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacterium/genética , Flavobacterium/isolamento & purificação , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
15.
Int J Syst Evol Microbiol ; 67(9): 3387-3392, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28857027

RESUMO

Little is known on members of the genus Amycolatopsis inhabiting acidic habitats. In this study, a moderately acidophilic Amycolatopsis strain, designated 2-5T, was isolated from coal mine soil, and subjected to a polyphasic taxonomic characterization. Analysis based on 16S rRNA gene sequences indicated that the strain was most closely related to the type strain of Amycolatopsis bartoniae, sharing 99.30 % similarity, while similarity to all other Amycolatopsis species was less than 97 %. The DNA-DNA relatedness between the new isolate and the type strain of A. bartoniae was 56.5±0.7 %. The optimal pH range of the isolate for growth was 5.5-6.0, but growth also occurred at pH 4.5 and 7.5. The isolate tolerated up to 6 % (w/v) NaCl (optimum, 0 %), and the temperature range for growth was 15-40 °C (optimum, 30 °C). The isolate was able to utilize most substrates tested for sole carbon sources, showing its metabolic versatility. The isolate exhibited antimicrobial activity against Serratia marcescens and weak antifungal activity against Fusarium proliferatum. The chemotaxonomic profiles of strain 2-5T included polar lipids containing phosphatidylethanolamine, phsphatidylmethylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol dimannosides, fatty acids containing C17 : 1ω6c and iso-C16 : 0 as the major components, MK-9(H4) as the predominant menaquinone, and meso-diaminopimelic acid and arabinose, galactose, glucose and ribose as the diagnostic diamino acid and sugars in the cell wall. The combined phenotypic, chemotaxonomic and genotypic analyses clearly indicated that the isolate merits recognition as represnting a novel species of Amycolatopsis, for which the name Amycolatopsis acidiphila sp. nov. is proposed. The type strain is 2-5T (=KCTC 39523T=JCM 30562T).


Assuntos
Actinomycetales/classificação , Minas de Carvão , Filogenia , Microbiologia do Solo , Actinomycetales/genética , Actinomycetales/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , Parede Celular/química , DNA Bacteriano/genética , DNA Ribossômico/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Mongólia , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
16.
Int J Syst Evol Microbiol ; 67(8): 3117-3121, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-28771125

RESUMO

A Gram-stain-negative, aerobic, oxidase-positive, catalase-positive and rod-shaped bacterium designated strain 3R17T was isolated from freshwater. Strain 3R17T produced bright-yellow, circular, convex and smooth colonies on R2A agar, tryptic soy agar, potato dextrose agar, nutrient agar and brain-heart infusion agar media. The strain was motile by gliding. The strain grew at 4-30 °C (optimum, 25 °C), at pH 6-9 (optimum, pH 7) and in the presence of up to 3 % NaCl (optimum, 0 %) on R2A agar. The 16S rRNA gene sequence analysis indicated that 3R17T represents a member of the genus Flavobacterium and is most closely related to Flavobacterium resistens BD-b365T, with a sequence similarity of 97.78 %, but the strain formed a distinct phylogenetic lineage of its own. Fatty acid analysis indicated that a summed feature comprising C16 : 1ω7c and/or C16 : 1ω6c, iso-C15 : 0, iso-C15 : 1G, anteiso-C15 : 0, C16 : 0, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH were the major components (>5 %). Strain 3R17T contained phosphatidylethanolamine (PE) and several unidentified aminolipids as main polar lipids, and MK-6 as the predominant isoprenoid quinone. Flexirubin pigments were not produced. The DNA G+C content was 35.4 mol%. The combination of physiological and chemotaxonomic properties distinguished 3R17T from related species of the genus Flavobacterium. On the basis of polyphasic taxonomy, 3R17T evidently represents a novel species within the genus Flavobacterium, for which the name Flavobacterium fluminis sp. nov. is proposed. The type strain is 3R17T (=KCTC 42062T=JCM 30338T).


Assuntos
Flavobacterium/classificação , Água Doce/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacterium/genética , Flavobacterium/isolamento & purificação , Fosfatidiletanolaminas/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
17.
Int J Syst Evol Microbiol ; 67(7): 2166-2170, 2017 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-28671526

RESUMO

A yellow-pigmented, oxidase-positive, catalase-negative, Gram-stain-negative, rod-shaped, aerobic and non-motile bacterial strain designated K3R-10T was isolated from a freshwater source. The strain grew over a temperature range from 4 to 35 °C (optimum, 30 °C), pH range pH 6-8 (optimum, pH 7) and in the presence of 0-0.5 % NaCl (optimum, 0 %). Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain K3R-10T belonged to the genus Flavobacterium and shared close similarities with Flavobacterium succinicans LMG 10402T (97.0 %), Flavobacterium chungangense LMG 26729T (96.4 %), Flavobacterium branchiophilum IFO 15030T (96.4 %) and Flavobacteriumpiscis412R-09T (96.3 %), but formed a distinct phylogenetic line of its own in the phylogenetic trees. The polar lipids consisted of phosphatidylethanolamine, an unidentified aminolipid and three unidentified phospholipids. The DNA G+C content was 35.4 mol%, MK-6 was the major isoprenoid quinone, and homospermidine was the predominant polyamine. The predominant cellular fatty acids were iso-C15 : 0 3-OH, iso-C15 : 0, a summed feature comprising C16 : 1ω7c and/or C16 : 1ω6c and iso-C15 : 1 G. The absence of aminophospholipid, acid production from carbohydrates, DNA G+C content and colony morphology differentiated strain K3R-10T from related species of the genus Flavobacterium. Thus, on the basis of phenotypic, chemotaxonomic and phylogenetic features, strain K3R-10T evidently represents a novel species in the genus Flavobacterium, for which the name Flavobacterium keumense sp. nov. is proposed. The type strain is K3R-10T (=JCM 31220T=KCTC 52563T).


Assuntos
Flavobacterium/classificação , Água Doce/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacterium/genética , Flavobacterium/isolamento & purificação , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Espermidina/química , Vitamina K 2/análogos & derivados , Vitamina K 2/química
18.
IEEE Trans Geosci Remote Sens ; Volume 55(Iss 4): 1897-1914, 2017 Jan 19.
Artigo em Inglês | MEDLINE | ID: mdl-31708601

RESUMO

This paper evaluates the retrieval of soil moisture in the top 5-cm layer at 3-km spatial resolution using L-band dual-copolarized Soil Moisture Active-Passive (SMAP) synthetic aperture radar (SAR) data that mapped the globe every three days from mid-April to early July, 2015. Surface soil moisture retrievals using radar observations have been challenging in the past due to complicating factors of surface roughness and vegetation scattering. Here, physically based forward models of radar scattering for individual vegetation types are inverted using a time-series approach to retrieve soil moisture while correcting for the effects of static roughness and dynamic vegetation. Compared with the past studies in homogeneous field scales, this paper performs a stringent test with the satellite data in the presence of terrain slope, subpixel heterogeneity, and vegetation growth. The retrieval process also addresses any deficiencies in the forward model by removing any time-averaged bias between model and observations and by adjusting the strength of vegetation contributions. The retrievals are assessed at 14 core validation sites representing a wide range of global soil and vegetation conditions over grass, pasture, shrub, woody savanna, corn, wheat, and soybean fields. The predictions of the forward models used agree with SMAP measurements to within 0.5 dB unbiased-root-mean-square error (ubRMSE) and -0.05 dB (bias) for both copolarizations. Soil moisture retrievals have an accuracy of 0.052 m3/m3 ubRMSE, -0.015 m3/m3 bias, and a correlation of 0.50, compared to in situ measurements, thus meeting the accuracy target of 0.06 m3/m3 ubRMSE. The successful retrieval demonstrates the feasibility of a physically based time series retrieval with L-band SAR data for characterizing soil moisture over diverse conditions of soil moisture, surface roughness, and vegetation.

19.
Int J Syst Evol Microbiol ; 66(8): 3230-3234, 2016 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-27222401

RESUMO

A Gram-stain-negative, motile by gliding, non-spore-forming and oval-shaped bacterial strain designated T1-10T was isolated from pine forest soil, and its taxonomic position was investigated using a polyphasic approach. Growth occurred at 10-37 °C (optimum, 30 °C), at pH 6-7 and in the presence of 0-1 % (w/v) (optimum, 0 %) NaCl. Flexirubin-type pigments were produced. On the basis of 16S rRNA gene sequence similarity, strain T1-10T was assigned to the genus Taibaiella of the phylum Bacteroidetes, and the most closely related species was Taibaiella koreensis THG-DT86T with 97.11 % sequence similarity, but the strain formed an independent lineage in the phylogenetic tree. The genomic DNA G+C content of strain T1-10T was 42.5 mol%. The main cellular fatty acids were iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH. The only isoprenoid quinone detected in the strain was MK-7, and the major polyamine was homospermidine. The major polar lipids were phosphatidylethanolamine and unidentified aminophospholipids. Strain T1-10T could be distinguished from related species by physiological and biochemical properties. Phenotypic and phylogenetic data supported that strain T1-10T represents a novel species of the genus Taibaiella, for which the name Taibaiella soli sp. nov. is proposed (type strain T1-10T=KCTC 42277T=JCM 31014T).


Assuntos
Bacteroidetes/classificação , Florestas , Filogenia , Pinus/microbiologia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfatidiletanolaminas , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Espermidina/química , Vitamina K 2/análogos & derivados , Vitamina K 2/química
20.
Int J Syst Evol Microbiol ; 66(7): 2509-2514, 2016 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-27081846

RESUMO

A novel actinobacterial strain, designated R1-20T, was isolated during a study of the bacterial diversity of the soil at a white heron nesting site. The isolate was non-motile, Gram-stain-positive and short rod-shaped. Colonies were dull white and convex with entire margin during the early stages of growth, and gradually became yellow. 16S rRNA gene sequence analysis indicated that the isolate belongs to the genus Humibacter of the family Microbacteriaceae, as sequence similarity with its nearest neighbours was 97.16 % with Humibacter antriD7-27Tand 96.44 % with Humibacter albusDSM 18994T. However, the combination of cultural and physiological as well as chemotaxonomic properties clearly distinguished strain R1-20T from other Humibacter species. The DNA G+C content of strain R1-20T was 65.5 mol%, and the major respiratory isoprenoid quinone was menaquinone MK-11. The acyl group of the peptidoglycan was of acetyl type, and the diagnostic diamino acid was 2,4-diaminobutyric acid. Glutamic acid, alanine and glycine were also present in the cell wall. The major fatty acids of strain R1-20T were anteiso-C17 : 0, iso-C16 : 0 and anteiso-C15 : 0. On the basis of phylogenetic, phenotypic and chemotaxonomic analysis, strain R1-20T merits recognition as a representative of a novel species of the genus Humibacter, for which the name Humibacter soli sp. nov. is proposed. The type strain is R1-20T (=KCTC 39614T=JCM 31015T).


Assuntos
Actinomycetales/classificação , Filogenia , Microbiologia do Solo , Actinomycetales/genética , Actinomycetales/isolamento & purificação , Aminobutiratos/química , Técnicas de Tipagem Bacteriana , Composição de Bases , Parede Celular/química , DNA Bacteriano/genética , Ácidos Graxos/química , Peptidoglicano/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/química
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA