scholarly journals High Levels of Endemicity of 3-Chlorobenzoate-Degrading Soil Bacteria

1998 ◽  
Vol 64 (5) ◽  
pp. 1620-1627 ◽  
Author(s):  
R. R. Fulthorpe ◽  
A. N. Rhodes ◽  
J. M. Tiedje
Keyword(s):  
South African ◽  
Boreal Forests ◽  
Soil Bacteria ◽  
Restriction Analysis ◽  
Mediterranean Ecosystems ◽  
Soil Samples ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Dna Restriction ◽  
Repetitive Extragenic Palindromic Pcr

ABSTRACT Soils samples were obtained from pristine ecosystems in six regions on five continents. Two of the regions were boreal forests, and the other four were Mediterranean ecosystems. Twenty-four soil samples from each of four or five sites in each of the regions were enriched by using 3-chlorobenzoate (3CBA), and 3CBA mineralizers were isolated from most samples. These isolates were analyzed for the ability to mineralize 3CBA, and genotypes were determined with repetitive extragenic palindromic PCR genomic fingerprints and restriction digests of the 16S rRNA genes (amplified ribosomal DNA restriction analysis [ARDRA]). We found that our collection of 150 stable 3CBA-mineralizing isolates included 48 genotypes and 44 ARDRA types, which formed seven distinct clusters. The majority (91%) of the genotypes were unique to the sites from which they were isolated, and each genotype was found only in the region from which it was isolated. A total of 43 of the 44 ARDRA types were found in only one region. A few genotypes were repeatedly found in one region but not in any other continental region, suggesting that they are regionally endemic. A correlation between bacterial genotype and vegetative community was found for the South African samples. These results suggest that the ability to mineralize 3CBA is distributed among very diverse genotypes and that the genotypes are not globally dispersed.

scholarly journals Extracellular hydrolytic enzyme production by proteolytic bacteria from the Antarctic

2013 ◽  
Vol 34 (3) ◽  
pp. 253-267 ◽  
Author(s):  
Mauro Tropeano ◽  
Susana Vázquez ◽  
Silvia Coria ◽  
Adrián Turjanski ◽  
Daniel Cicero ◽  
...  
Keyword(s):  
Extracellular Enzymes ◽  
Restriction Analysis ◽  
Hydrolytic Enzyme ◽  
Hydrolytic Enzymes ◽  
Extracellular Enzyme ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Potter Cove ◽  
Starting Point ◽  
Dna Restriction

AbstractCold−adapted marine bacteria producing extracellular hydrolytic enzymes are important for their industrial application and play a key role in degradation of particulate organic matter in their natural environment. In this work, members of a previously−obtained protease−producing bacterial collection isolated from different marine sources from Potter Cove (King George Island, South Shetlands) were taxonomically identified and screened for their ability to produce other economically relevant enzymes. Eighty−eight proteolytic bacterial isolates were grouped into 25 phylotypes based on their Amplified Ribosomal DNA Restriction Analysis profiles. The sequencing of the 16S rRNA genes from representative isolates of the phylotypes showed that the predominant culturable protease−producing bacteria belonged to the class Gammaproteobacteria and were affiliated to the genera Pseudomonas, Shewanella, Colwellia, and Pseudoalteromonas, the latter being the predominant group (64% of isolates). In addition, members of the classes Actinobacteria, Bacilli and Flavobacteria were found. Among the 88 isolates screened we detected producers of amylases (21), pectinases (67), cellulases (53), CM−cellulases (68), xylanases (55) and agarases (57). More than 85% of the isolates showed at least one of the extracellular enzymatic activities tested, with some of them producing up to six extracellular enzymes. Our results confirmed that using selective conditions to isolate producers of one extracellular enzyme activity increases the probability of recovering bacteria that will also produce additional extracellular enzymes. This finding establishes a starting point for future programs oriented to the prospecting for biomolecules in Antarctica.

scholarly journals APLIKASI METODE ARDRA DALAM IDENTIFIKASI ISOLAT Bacillus thuringiensis ENDOGENIK SEBAGAI PENGENDALI HAMA KUBIS (Crocidolomia binotalis)

EUGENIA ◽  
2011 ◽  
Vol 17 (2) ◽  
Author(s):  
Christina L. Salaki ◽  
Langkah Sembiring
Keyword(s):  
Profile Analysis ◽  
Restriction Analysis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Universal Primers ◽  
Chromosomal Dna ◽  
Pcr Products ◽  
Agarose Electrophoresis ◽  
Electrophoresis Method ◽  
Dna Restriction

ABSTRACT Indonesian indigenous bacterial isolates of B. thuringiensis pathogenic to cabbage pest (C. binotalis) were molecularly characterized and identified using DNA fingerprinting method of ARDRA (Amplified Ribosomal DNA Restriction Analysis). Chromosomal DNA of 10 selected isolates (SLK2.3, SRNG4.2, TKO1, TK9, YPPA1, UG1A, BLPPN8.2, YWKA1, BAU3.2, LPST1) and 2 reference strains (B. thuringiensis serovar kurstaki HD1 & B. thuringiensis serovar israelensis H14) were isolated and purified by standard method. 16S rRNA genes were amplified by PCR method using universal primers of 27f and 1529r. PCR products were digested by 4 restriction endonucleases (EcoR1, HindIII, Pst1 dan HaeIII), and separated by agarose electrophoresis method to generate ARDRA profiles. Results of study showed that only ARDRA profiles generated by Hae III digestion were found to be meaningful and therefore used to identify the isolates. The ARDRA profile analysis indicated that the reference strain of B. thuringiensis serovar kurstaki HD1 could be clearly separated with B. thuringiensis serovar israelensis H14. In fact, those two strains have been widely recognized to be different in terms of their pathogenic specifity against insects. B. thuringiensis serovar kurstaki HD1 has been known to be specifically pathogenic to Lepidopteran whereas B. thuringiensis serovar israelensis H14 has been known to be specifically pathogenic to Dipteran. Key words : application, ARDRA, indigenous, B. thuringiensis, C. binotalis  

Diversity of Bacillus Species Isolated from Okpehe, a Traditional Fermented Soup Condiment from Nigeria

2010 ◽  
Vol 73 (5) ◽  
pp. 870-878 ◽  
Author(s):  
FOLARIN A. OGUNTOYINBO ◽  
MELANIE HUCH ◽  
GYU-SUNG CHO ◽  
ULRICH SCHILLINGER ◽  
WILHELM H. HOLZAPFEL ◽  
...  
Keyword(s):  
Restriction Analysis ◽  
Restriction Enzymes ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacillus Species ◽  
Fermented Foods ◽  
Potential Health ◽  
Enterotoxin Genes ◽  
Bacillus Spp ◽  
Dna Restriction

The diversity of Bacillus species isolated from the fermented soup condiment okpehe in Nigeria was studied using a combination of phenotypic and genotypic methods. Fifty strains presumptively characterized as Bacillus spp. using the API 50 CHB test were further identified by PCR of randomly amplified polymorphic DNA (RAPD) and by amplified ribosomal DNA restriction analysis (ARDRA) genotyping methods. ARDRA fingerprinting with HhaI, HinfI, and Sau3AI restriction enzymes did not allow successful differentiation between the Bacillus species, except for distinguishing B. cereus from other Bacillus species. This problem was overcome with the combination of RAPD PCR and ARDRA genotypic fingerprinting techniques. Sequencing of 16S rRNA genes of selected strains representative of the major clusters revealed that the Bacillus strains associated with this fermentation were B. subtilis, B. amyloliquefaciens, B. cereus, and B. licheniformis (in decreasing order of incidence). The presence of enterotoxin genes in all B. cereus strains was demonstrated by multiplex PCR. The high incidence of detection (20%) of possibly pathogenic B. cereus strains that contained enterotoxin genes indicated that these fermented foods may constitute a potential health risk.

Abundance, diversity and mobility potential of antibiotic resistance genes in pristine Tibetan Plateau soil as revealed by soil metagenomics

2020 ◽  
Vol 96 (10) ◽  
Author(s):  
Bo Li ◽  
Zeng Chen ◽  
Fan Zhang ◽  
Yongqin Liu ◽  
Tao Yan
Keyword(s):  
Antibiotic Resistance ◽  
Microbial Diversity ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Soil Samples ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Metagenomic Sequencing ◽  
Clinical Issue ◽  
Abundance And Diversity

ABSTRACT Widespread occurrence of antibiotic resistance genes (ARGs) has become an important clinical issue. Studying ARGs in pristine soil environments can help to better understand the intrinsic soil resistome. In this study, 10 soil samples were collected from a high elevation and relatively pristine Tibetan area, and metagenomic sequencing and bioinformatic analyses were conducted to investigate the microbial diversity, the abundance and diversity of ARGs and the mobility potential of ARGs as indicated by different mobile genetic elements (MGEs). A total of 48 ARG types with a relative abundance of 0.05–0.28 copies of ARG/copy of 16S rRNA genes were detected in Tibetan soil samples. The observed ARGs were mainly associated with antibiotics that included glycopeptide and rifamycin; the most abundant ARGs were vanRO and vanSO. Low abundance of MGEs and potentially plasmid-related ARGs indicated a low horizontal gene transfer risk of ARGs in the pristine soil. Pearson correlation and redundancy analyses showed that temperature and total organic carbon were the major environmental factors controlling both microbial diversity and ARG abundance and diversity.

scholarly journals Genetic and Biochemical Diversity among Isolates ofPaenibacillus alvei Cultured from Australian Honeybee (Apis mellifera) Colonies

2000 ◽  
Vol 66 (3) ◽  
pp. 1098-1106 ◽  
Author(s):  
Steven P. Djordjevic ◽  
Wendy A. Forbes ◽  
Lisa A. Smith ◽  
Michael A. Hornitzky
Keyword(s):  
Apis Mellifera ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Restriction Analysis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Whole Cell ◽  
Restriction Profiles ◽  
Dna Profiles

ABSTRACT Twenty-five unique CfoI-generated whole-cell DNA profiles were identified in a study of 30 Paenibacillus alvei isolates cultured from honey and diseased larvae collected from honeybee (Apis mellifera) colonies in geographically diverse areas in Australia. The fingerprint patterns were highly variable and readily discernible from one another, which highlighted the potential of this method for tracing the movement of isolates in epidemiological studies. 16S rRNA gene fragments (length, 1,416 bp) for all 30 isolates were enzymatically amplified by PCR and subjected to restriction analysis with DraI, HinfI,CfoI, AluI, FokI, andRsaI. With each enzyme the restriction profiles of the 16S rRNA genes from all 30 isolates were identical (one restriction fragment length polymorphism [RFLP] was observed in theHinfI profile of the 16S rRNA gene from isolate 17), which confirmed that the isolates belonged to the same species. The restriction profiles generated by using DraI,FokI, and HinfI differentiated P. alvei from the phylogenetically closely related speciesPaenibacillus macerans and Paenibacillus macquariensis. Alveolysin gene fragments (length, 1,555 bp) were enzymatically amplified from some of the P. alvei isolates (19 of 30 isolates), and RFLP were detected by using the enzymesCfoI, Sau3AI, and RsaI. Extrachromosomal DNA ranging in size from 1 to 10 kb was detected in 17 of 30 (57%) P. alvei whole-cell DNA profiles. Extensive biochemical heterogeneity was observed among the 28 P. alvei isolates examined with the API 50CHB system. All of these isolates were catalase, oxidase, and Voges-Proskauer positive and nitrate negative, and all produced acid when glycerol, esculin, and maltose were added. The isolates produced variable results for 16 of the 49 biochemical tests; negative reactions were recorded in the remaining 30 assays. The genetic and biochemical heterogeneity inP. alvei isolates may be a reflection of adaptation to the special habitats in which they originated.

scholarly journals Diversity of Lactic Acid Bacteria Associated with Fish and the Fish Farm Environment, Established by Amplified rRNA Gene Restriction Analysis

2007 ◽  
Vol 73 (9) ◽  
pp. 2947-2955 ◽  
Author(s):  
Christian Michel ◽  
Claire Pelletier ◽  
Mekki Boussaha ◽  
Diane-Gaëlle Douet ◽  
Armand Lautraite ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Opportunistic Infections ◽  
Restriction Analysis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Fish Food ◽  
Group A ◽  
Gene Restriction

ABSTRACT Lactic acid bacteria have become a major source of concern for aquaculture in recent decades. In addition to true pathogenic species of worldwide significance, such as Streptococcus iniae and Lactococcus garvieae, several species have been reported to produce occasional fish mortalities in limited geographic areas, and many unidentifiable or ill-defined isolates are regularly isolated from fish or fish products. To clarify the nature and prevalence of different fish-associated bacteria belonging to the lactic acid bacterium group, a collection of 57 isolates of different origins was studied and compared with a set of 22 type strains, using amplified rRNA gene restriction analysis (ARDRA). Twelve distinct clusters were delineated on the basis of ARDRA profiles and were confirmed by sequencing of sodA and 16S rRNA genes. These clusters included the following: Lactococcus raffinolactis, L. garvieae, Lactococcus l., S. iniae, S. dysgalactiae, S. parauberis, S. agalactiae, Carnobacterium spp., the Enterococcus “faecium” group, a heterogeneous Enterococcus-like cluster comprising indiscernible representatives of Vagococcus fluvialis or the recently recognized V. carniphilus, V. salmoninarum, and Aerococcus spp. Interestingly, the L. lactis and L. raffinolactis clusters appeared to include many commensals of fish, so opportunistic infections caused by these species cannot be disregarded. The significance for fish populations and fish food processing of three or four genetic clusters of uncertain or complex definition, namely, Aerococcus and Enterococcus clusters, should be established more accurately.

scholarly journals Laboratory Cultivation of Widespread and Previously Uncultured Soil Bacteria

2003 ◽  
Vol 69 (12) ◽  
pp. 7210-7215 ◽  
Author(s):  
Shayne J. Joseph ◽  
Philip Hugenholtz ◽  
Parveen Sangwan ◽  
Catherine A. Osborne ◽  
Peter H. Janssen
Keyword(s):  
Soil Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Phylogenetic Groups ◽  
Bacterial Phyla ◽  
New Family ◽  
Solid Media ◽  
Family Level ◽  
Petri Dishes ◽  
High Degree

ABSTRACT Most soil bacteria belong to family-level phylogenetic groups with few or no known cultivated representatives. We cultured a collection of 350 isolates from soil by using simple solid media in petri dishes. These isolates were assigned to 60 family-level groupings in nine bacterial phyla on the basis of a comparative analysis of their 16S rRNA genes. Ninety-three (27%) of the isolates belonged to 20 as-yet-unnamed family-level groupings, many from poorly studied bacterial classes and phyla. They included members of subdivisions 1, 2, 3, and 4 of the phylum Acidobacteria, subdivision 3 of the phylum Verrucomicrobia, subdivision 1 of the phylum Gemmatimonadetes, and subclasses Acidimicrobidae and Rubrobacteridae of the phylum Actinobacteria. In addition, members of 10 new family-level groupings of subclass Actinobacteridae of the phylum Actinobacteria and classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria of the phylum Proteobacteria were obtained. The high degree of phylogenetic novelty and the number of isolates affiliated with so-called unculturable groups show that simple cultivation methods can still be developed further to obtain laboratory cultures of many phylogenetically novel soil bacteria.

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