scholarly journals Detection and Isolation of Novel Rhizopine-Catabolizing Bacteria from the Environment

1998 ◽  
Vol 64 (12) ◽  
pp. 4944-4949 ◽  
Author(s):  
Brian B. McSpadden Gardener ◽  
Frans J. de Bruijn
Keyword(s):  
Dna Sequences ◽  
Sinorhizobium Meliloti ◽  
Southern Hybridization ◽  
Southern Hybridization Analysis ◽  
Carbon And Nitrogen ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Standard Assay ◽  
Ribosomal Dnas ◽  
Assay Conditions

ABSTRACT Microbial rhizopine-catabolizing (Moc) activity was detected in serial dilutions of soil and rhizosphere washes. The activity observed generally ranged between 106 and 107 catabolic units per g, and the numbers of nonspecific culture-forming units were found to be approximately 10 times higher. A diverse set of 37 isolates was obtained by enrichment on scyllo-inosamine-containing media. However, none of the bacteria that were isolated were found to contain DNA sequences homologous to the known mocA,mocB, and mocC genes of Sinorhizobium meliloti L5-30. Twenty-one of the isolates could utilize an SI preparation as the sole carbon and nitrogen source for growth. Partial sequencing of 16S ribosomal DNAs (rDNAs) amplified from these strains indicated that five distinct bacterial genera (Arthrobacter, Sinorhizobium,Pseudomonas, Aeromonas, andAlcaligenes) were represented in this set. Only 6 of these 21 isolates could catabolize 3-O-methyl-scyllo-inosamine under standard assay conditions. Two of these, strains D1 and R3, were found to have 16S rDNA sequences very similar to those of Sinorhizobium meliloti. However, these strains are not symbiotically effective on Medicago sativa, and DNA sequences homologous to thenodB and nodC genes were not detected in strains D1 and R3 by Southern hybridization analysis.

Rapid identification of Medicago nodulating strains by using two oligonucleotide probes complementary to 16S rDNA sequences

1997 ◽  
Vol 43 (9) ◽  
pp. 854-861 ◽  
Author(s):  
Sophie Rome ◽  
Jean-Claude Cleyet-Marel ◽  
Luis A. Materon ◽  
Philippe Normand ◽  
Brigitte Brunel
Keyword(s):  
16S Rdna ◽  
Sinorhizobium Meliloti ◽  
Bacterial Species ◽  
Blot Hybridization ◽  
Dot Blot ◽  
Plant Host ◽  
Rdna Sequences ◽  
Sinorhizobium Medicae ◽  
16S Rdna Sequences ◽  
Annual Medicago

Symbiotic bacteria associated with the Medicago genus are separated into two closely related species named Sinorhizobium meliloti and Sinorhizobium medicae. To discriminate rapidly between these two bacterial species, two 15-base DNA probes, 16Smfs and 16Smed, were designed from the alignment of 16S rDNA sequences to differentiate S. meliloti from S. medicae. Their specificities were evaluated by dot-blot hybridization experiments on 25 reference strains representing 13 species of Rhizobium and Sinorhizobium, and by comparison with all 16S rDNA sequences available in the GenBank data base. No cross-reaction was found with 16Smed, which was thus considered species specific for S. medicae. By contrast, as expected according to the 16S rDNA sequence alignment, the labeled 16Smfs probe cross-hybridized with the DNAs of S. meliloti, Sinorhizobium fredii, and Sinorhizobium saheli but not with the DNA of S. medicae. Since S. saheli and S. fredii do not nodulate Medicago, 16Smed and 16Smfs can be routinely used to characterize the two Sinorhizobium species nodulating Medicago from pure cultures or from Medicago root nodules. Fifty strains isolated from eight annual Medicago species were then characterized by using colony hybridizations. Sinorhizobium meliloti was more frequently obtained (>80% isolates) than was S. medicae. Both Sinorhizobium species seemed to be trapped by annual Medicago and no plant-host specificity was detected.Key words: Sinorhizobium meliloti, Sinorhizobium medicae, Medicago, oligonucleotide probe, 16S rDNA gene.

Anaerobic oxidation of cholesterol by a denitrifying enrichment

2001 ◽  
Vol 44 (4) ◽  
pp. 145-150 ◽  
Author(s):  
E. Barrandeguy ◽  
S. Tarlera
Keyword(s):  
Anaerobic Treatment ◽  
Organic Load ◽  
Cholesterol Oxidation ◽  
Nitrite Accumulation ◽  
Reactor Performance ◽  
Nitrogen Gas ◽  
Carbon And Nitrogen ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
The One

Sterols (e.g. cholesterol) present in wool scouring effluent represent the most recalcitrant fraction in anaerobic treatment. This study was conducted to examine the feasibility of removal of this organic load through a denitrifying post-treatment stage. A stable cholesterol-denitrifying enrichment (CHOL-1) was obtained from sludge of a bench-scale upflow sludge bed (USB) denitrifying reactor integrated to a carbon and nitrogen removal system for sanitary landfill leachate. According to the amounts of cholesterol degraded and of nitrite and nitrogen gas formed, the capacity for complete cholesterol oxidation under anaerobic conditions by CHOL-1 can be assumed. Nitrite accumulation observed at a low C/N ratio outlines the importance of determining the optimal C/N ratio for adequate denitrifying reactor performance. The enrichment was partly identified with molecular analysis of cloned 16S rDNA sequences revealing the presence of two groups of bacteria belonging to the β subclass of the Proteobacteria. According to analysis of sequences, it can be inferred that a yet uncultivated new bacterium is the one responsible for cholesterol oxidation. Results of this study suggest that sludge from a denitrifying reactor treating leachate is potentially useful in a combined anaerobic-anoxic system for degradation of cholesterol that remains after methanogenic treatment.

scholarly journals Bacterial DNA Diversity among Clear and Cloudy Sakes, and Sake-kasu

2020 ◽  
Vol 13 (1) ◽  
pp. 74-82
Author(s):  
Momoka Terasaki ◽  
Hiromi Nishida
Keyword(s):  
Production Process ◽  
Dna Sequences ◽  
Bacterial Contamination ◽  
Yeast Cells ◽  
Bacterial Cells ◽  
Bacterial Dna ◽  
Rdna Sequences ◽  
Dna Diversity ◽  
16S Rdna Sequences ◽  
The Difference

Background: The traditional Japanese alcoholic drink, sake, is classified into two types: those that contain sediment produced during the production process (cloudy sakes) and those that do not contain such sediment (clear sakes). Leftover pressed sediment from the sake production process, sake-kasu (sake cake or sake lees), is commercially available and is highly nutritious for humans. Objective: The purpose of this study was to determine the difference among component bacterial DNA sequences of clear and cloudy sakes, and sake-kasu. Methods: We compared the 16S rDNA sequences from 44 samples of clear sake, 3 samples of cloudy sake, and 11 samples of sake-kasu. Results: The DNA sequences were divided into three major clusters; however, sequences in sake-kasu were located in just one cluster forming two lineages. The microbial diversity in sake-kasu was lower than that in clear and cloudy sakes, which may be because some of the contaminating bacterial cells do not lyse during the production process and remain intact, along with yeast cells, in sake-kasu. Conclusion: Bacterial DNA frequently detected in sake samples was from environmental bacterial contamination that occurs early in the sake production process. Contaminating bacteria are usually killed by the ethanol produced as the sake yeast grows; after which, if bacteria lyse, the bacterial DNA is released into the sake solution. However, if the bacterial cells do not lyse, they will precipitate toward the sediment. Thus, there is bacterial DNA diversity in clear and cloudy sake, but less diversity in sake-kasu.

scholarly journals Retention of relict satellite DNA sequences in Anemone (Ranunculaceae)

2013 ◽  
Vol 72 (1) ◽  
pp. 1-133 ◽  
Author(s):  
Višnja Besendorfer ◽  
Jelena Mlinarec
Keyword(s):  
Dna Sequences ◽  
Southern Hybridization ◽  
Repeat Unit ◽  
Similar Species ◽  
Genomic Component ◽  
Library Hypothesis ◽  
Species Specific ◽  
Eukaryotic Organisms ◽  
Fish Signal

Abstract Satellite DNAis a genomic component present in virtually all eukaryotic organisms. The turnover of highly repetitive satellite DNAis an important element in genome organization and evolution in plants. Here we study the presence, physical distribution and abundance of the satellite DNAfamily AhTR1 in Anemone. Twenty-two Anemone accessions were analyzed by PCR to assess the presence of AhTR1, while fluorescence in situ hybridization and Southern hybridization were used to determine the abundance and genomic distribution of AhTR1. The AhTR1 repeat unit was PCR-amplified only in eight phylogenetically related European Anemone taxa of the Anemone section. FISH signal with AhTR1 probe was visible only in A. hortensis and A. pavonina, showing localization of AhTR1 in the regions of interstitial heterochromatin in both species. The absence of a FISH signal in the six other taxa as well as weak signal after Southern hybridization suggest that in these species AhTR1 family appears as relict sequences. Thus, the data presented here support the »library hypothesis« for AhTR1 satellite evolution in Anemone. Similar species-specific satellite DNAprofiles in A. hortensis and A. pavonina support the treatment of A. hortensis and A. pavonina as one species, i.e. A. hortensis s.l.

scholarly journals The phylogeny of the genusYersiniabased on 16S rDNA sequences

1993 ◽  
Vol 114 (2) ◽  
pp. 173-177 ◽  
Author(s):  
A. Ibrahim ◽  
B.M. Goebel ◽  
W. Liesack ◽  
M. Griffiths ◽  
E. Stackebrandt
Keyword(s):  
16S Rdna ◽  
Rdna Sequences ◽  
16S Rdna Sequences

Carboxymethylhydroxymuconic semialdehyde dehydrogenase in the 4-hydroxyphenylacetate catabolic pathway of Pseudomonas putida

1986 ◽  
Vol 64 (12) ◽  
pp. 1288-1293 ◽  
Author(s):  
Josefa M. Alonso ◽  
Amando Garrido-Pertierra
Keyword(s):  
Pseudomonas Putida ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Gel Filtration ◽  
Competitive Inhibitor ◽  
Catabolic Pathway ◽  
Ph Optimum ◽  
Semialdehyde Dehydrogenase ◽  
Standard Assay ◽  
Assay Conditions

5-Carboxymethyl-2-hydroxymuconic semialdehyde (CHMSA) dehydrogenase in the 4-hydroxyphenylacetate meta-cleavage pathway was purified from Pseudomonas putida by gel filtration, anion-exchange, and affinity chromatographies. Sodium dodecyl sulfate – polyacrylamide gel electrophoresis analysis suggested an approximate tetrameric molecular weight of 200 000. The purified enzyme showed a pH optimum at 7.8. The temperature–activity relationship for the enzyme from 27 to 45 °C showed broken Arrhenius plots with an inflexion at 36–37 °C. Under standard assay conditions, the enzyme acted preferentially with NAD. It could also catalyze the reduction with NADP (which had a higher Km), at 18% of the rate observed for NAD. The following kinetic parameters were found: Km(NAD) = 20.0 ± 3.6 μM, Km(CHMSA) = 8.5 ± 1.8 μM, and Kd(enzyme–NAD complex) = 7.8 ± 2.0 μM. The product NADH acted as a competitive inhibitor against NAD.

scholarly journals Molecular analysis of the microflora in chronic venous leg ulceration

2003 ◽  
Vol 52 (4) ◽  
pp. 365-369 ◽  
Author(s):  
K.E. Hill ◽  
C.E. Davies ◽  
M.J. Wilson ◽  
P. Stephens ◽  
K.G. Harding ◽  
...  
Keyword(s):  
Individual Species ◽  
Venous Leg Ulcer ◽  
Bacterial Populations ◽  
Cultural Methods ◽  
Rdna Sequences ◽  
Oral Microflora ◽  
16S Rdna Sequences ◽  
First Time

There is growing evidence to suggest that the resident microflora of chronic venous leg ulcers impairs cellular wound-healing responses, thereby playing an important role in maintaining the non-healing phenotype of many of these wounds. The significance of individual species of bacteria will remain unclear until it is possible to characterize fully the microflora of such lesions. The limitations and biases of culture-based microbiology are being realized and the subsequent application of molecular methods is revealing greater diversity within mixed bacterial populations than that demonstrated by culture alone. To date, this approach has been limited to a small number of systems, including the oral microflora. Here, for the first time, the comprehensive characterization of the microflora present in the tissue of a chronic venous leg ulcer is described by the comparison of 16S rDNA sequences amplified directly from the wound tissue with sequences obtained from bacteria that were isolated by culture. The molecular approach demonstrated significantly greater bacterial diversity than that revealed by culture. Furthermore, sequences were retrieved that may possibly represent novel species of bacteria. It is only by the comprehensive analysis of the wound microflora by both molecular and cultural methods that it will be possible to further our understanding of the role of bacteria in this important condition.

scholarly journals Isolation and Identification of Hydrocarbon-Degrading Bacteria that Tolerant to Saponin of Sapindus Rarak Plant

2019 ◽  
Vol 4 (1) ◽  
pp. 79-88
Author(s):  
Evi Octaviany ◽  
Suharjono Suharjono ◽  
Irfan Mustafa
Keyword(s):  
Crude Oil ◽  
16S Rdna ◽  
Bacterial Isolates ◽  
High Concentration ◽  
Isolation And Identification ◽  
Rdna Sequences ◽  
Degrading Bacteria ◽  
16S Rdna Sequences ◽  
Petroleum Contaminated Soil ◽  
Cell Densities

A commercial saponin as biosurfactant can reduce the surface tension of water and increase of hydrocarbon degradation. However, this saponin can be toxic to some hydrocarbonoclastic bac-teria. This study aimed to obtain bacterial isolates that were tolerant and incapable to degrade saponin, and to identify them based on 16S rDNA sequence. Bacteria were isolated from petroleum contaminated soil in Wonocolo Village, Bojonegoro Regency, East Java, Indonesia. The soil samples were acclimated using Bushnell-Haas (BH) broth with 0.5% crude oil at room temperature for 3 weeks. The culture was spread onto BH agar incubated at 30°C for 7 days. The first screened, isolates were grown in nutrient broth with addition of sap-onin 0%, 8%, and 12% (v/v) then incubated at 30°C for three days. The bacterial cell density was measured using a spectrophotometer. Second screened, the isolates were grown on BH broth with addition of 0.5% saponin as a sole carbon source, and their cell densities were measured. The selected isolates were identified based on 16S rDNA sequences. Among 34 bacterial isolates, nine isolates were tol-erant to 12% saponin. Three bacterial isolates IHT1.3, IHT1.5, and IHT3.24 tolerant to high concentration of saponin and did not use this substance as growth nutrition. The IHT1.3, IHT1.5, and IHT3.24 isolates were identified as Ochrobactrum pseudogrignonense (99% similarity), Pseudomonas mendocina (99%), and Ochrobactrum pi-tuitosum; (97%), respectively. Those three selected isolates are good candidates as hydrocarbon-degrading bacteria to bioremediation of soil contaminated crude oil. However, the combined activity of bacteria and saponin to degrade hydrocarbon needs further study. 

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