The identification and genetic diversity of endophytic bacteria isolated from selected crops

2018 ◽  
Vol 156 (4) ◽  
pp. 547-556 ◽  
Author(s):  
M. Woźniak ◽  
A. Gałązka ◽  
J. Grządziel ◽  
M. Głodowska
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Agricultural Soils ◽  
16S Rrna Gene Sequencing ◽  
Genomic Diversity ◽  
Wild Plants ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Gradient Gel Electrophoresis ◽  
Rrna Gene Sequencing ◽  
Degree Of Differentiation

AbstractA collection of 45 isolates was created based on bacteria isolated from maize, broad bean, wheat, rye and wild plants such as horsetail and burdock. The aim of the current study was to isolate the bacteria, and then identify and assess the degree of genomic diversity. The molecular identification of microsymbionts isolated from the endosphere (root and stem) of plants grown in agricultural soils was performed using 16S rRNA gene sequencing. To evaluate the genomic diversity between strains that occurred in multiple host plants, 18 bacterial isolates representing four species were subjected to denaturing gradient gel electrophoresis. The 16S rDNA analysis assigned all bacterial isolates to ten genera, from whichRhizobiumwas represented by 19 isolates,Delftiaby 11,Agrobacteriumby five,Stenotrophomonasby three,Brevundimonasby two andNovosphingobium,Variovorax, Collimonas, AchromobacterandComamonasby only one isolate. Furthermore, the genomic diversity of the 11 isolates ofDelftiasp. was assessed using the BOX – polymerase chain reaction (BOX-PCR) and enterobacterial repetitive intergenic consensus – PCR (ERIC-PCR) methods. Typing patterns and analysis using BOX-PCR and ERIC-PCR data demonstrated similarities among the tested isolates. In general, the results obtained with BOX-PCR and ERIC-PCR were in good agreement. However, a greater degree of differentiation patterns of the genomic DNA was obtained in the ERIC-PCR method.

scholarly journals Influence of Particle Size on Bacterial Community Structure in Aquatic Sediments as Revealed by 16S rRNA Gene Sequence Analysis

2008 ◽  
Vol 74 (16) ◽  
pp. 5237-5240 ◽  
Author(s):  
Colin R. Jackson ◽  
Andrew Q. Weeks
Keyword(s):  
Particle Size ◽  
Community Structure ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Denaturing Gradient Gel Electrophoresis ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Gradient Gel Electrophoresis ◽  
Rrna Gene Sequencing

ABSTRACT Bacterial communities associated with sediment particles were examined using PCR-denaturing gradient gel electrophoresis and 16S rRNA gene sequencing. Particle size influenced community structure, with attached bacterial assemblages separating into 63- to 125-, 125- to 1,000-, and 1,000- to 2,000-μm fractions. Differences were particularly pronounced for the Verrucomicrobia-Planctomycetes, whose numbers were significantly reduced on coarser particles.

scholarly journals Succession of Selected Strains of Acetobacter pasteurianus and Other Acetic Acid Bacteria in Traditional Balsamic Vinegar

2009 ◽  
Vol 75 (8) ◽  
pp. 2585-2589 ◽  
Author(s):  
Maria Gullo ◽  
Luciana De Vero ◽  
Paolo Giudici
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Acetic Acid Bacteria ◽  
Rrna Gene ◽  
Enterobacterial Repetitive Intergenic Consensus ◽  
Acetobacter Pasteurianus ◽  
Gradient Gel Electrophoresis ◽  
Balsamic Vinegar ◽  
Rrna Gene Sequencing

ABSTRACT The application of a selected Acetobacter pasteurianus strain for traditional balsamic vinegar production was assessed. Genomic DNA was extracted from biofilms after enrichment cultures on GYC medium (10% glucose, 1.0% yeast extract, 2.0% calcium carbonate) and used for PCR/denaturing gradient gel electrophoresis, 16S rRNA gene sequencing, and enterobacterial repetitive intergenic consensus/PCR sequencing. Results suggested that double-culture fermentation is suitable for traditional balsamic vinegar acetification.

scholarly journals Assessment and Characterization of Xylanolytic Bacteria Isolated from the Gut of Microtermes Obesi for Biomass Pretreatment

2021 ◽  
Author(s):  
Iram Batool ◽  
Falak Sher Khan ◽  
Muhammad Awais ◽  
Dawood Ahmed ◽  
Sami Ullah Khan ◽  
...  
Keyword(s):  
Corn Stover ◽  
Rice Straw ◽  
16S Rrna Gene Sequencing ◽  
Major Constituent ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Cotton Stalk ◽  
Termite Gut ◽  
Chemical Pretreatments ◽  
Rrna Gene Sequencing

Abstract The aim of current research was to examine the potential for the production of hemicelluloses degrading enzymes from bacteria harbor in termite gut. The research was also focused on the conversion of lignocellulosic biomass (Corn stover, rice straw and cotton stalk) into fermentable sugars by using enzymes from the bacterial isolates. The bacterial isolates from termite gut were screened for their ability to degrade xylan that is the major constituent of hemicelluloses. Two bacterial isolates were chosen and identified by 16S rRNA gene sequencing. Both isolates TGB9 and TGB10 belong to Bacillus geneus. The isolates have shown higher xylan degrading activity at 50 oC and optimum pH was 6.0. Xylanases from isolate TGB9 and TGB10 were utilized for sccharification of agricultural substrates (stover, rice straw and cotton stalk). As a result higher contents of reducing sugars were observed from corn stover. Xylanases from isolate TGB9 produced higher yields of reducing sugar than isolate TGB10. A comparative study was also performed among chemical pretreatment and xylanases from bacterial isolates. For this purpose agricultural substrates were also treated with H2SO4 and NaOH. Xylanases produced by TGB9 and TGB10 released higher content of sugar from agricultural substrates than chemical pretreatments. So it is concluded that termite gut have bacteria that can hydrolyze hemicelluloses more efficiently than chemicals.

scholarly journals Profiling the microbial community of a Triassic halite deposit in Northern Ireland: an environment with significant potential for biodiscovery

2019 ◽  
Vol 366 (22) ◽  
Author(s):  
Julianne Megaw ◽  
Stephen A Kelly ◽  
Thomas P Thompson ◽  
Timofey Skvortsov ◽  
Brendan F Gilmore
Keyword(s):  
Northern Ireland ◽  
16S Rrna Gene Sequencing ◽  
Antimicrobial Activities ◽  
Chemical Diversity ◽  
Hypersaline Environment ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Culture Independent ◽  
Rrna Gene Sequencing ◽  
County Antrim

ABSTRACT Kilroot salt mine, a Triassic halite deposit located in County Antrim, Northern Ireland, is the only permanent hypersaline environment on the island of Ireland. In this study, the microbiome of this unstudied environment was profiled for the first time using conventional and enhanced culturing techniques, and culture independent metagenomic approaches. Using both conventional isolation plates and iChip devices, 89 halophilic archaeal isolates from six known genera, and 55 halophilic or halotolerant bacterial isolates from 18 genera were obtained, based on 16S rRNA gene sequencing. The archaeal isolates were similar to those previously isolated from other ancient halite deposits, and as expected, numerous genera were identified in the metagenome which were not represented among the culturable isolates. Preliminary screening of a selection of isolates from this environment identified antimicrobial activities against a panel of clinically important bacterial pathogens from 15 of the bacterial isolates and one of the archaea. This, alongside previous studies reporting the discovery of novel biocatalysts from the Kilroot mine microbiome, suggests that this environment may be a new, untapped source of of chemical diversity with high biodiscovery potential.

Chitinolytic bacteria in the intestinal tract of Japanese coastal fishes

2006 ◽  
Vol 52 (12) ◽  
pp. 1158-1163 ◽  
Author(s):  
Shiro Itoi ◽  
Toshihiro Okamura ◽  
Yuki Koyama ◽  
Haruo Sugita
Keyword(s):  
16S Rrna ◽  
Intestinal Tract ◽  
Intestinal Bacteria ◽  
16S Rrna Gene Sequencing ◽  
Colloidal Chitin ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Coastal Fish ◽  
Chitinolytic Bacteria ◽  
Rrna Gene Sequencing

Intestinal bacteria from several coastal fish species were screened on 1/20 PYBG medium containing 0.2% colloidal chitin, and 361 bacteria capable of decomposing colloidal chitin were isolated. These isolates were subsequently screened on media containing either 0.5% α-chitin or 0.5% β-chitin resulting in the identification of 31 α-chitinolytic and 275 β-chitinolytic bacterial isolates. Partial 16S rRNA gene sequencing was carried out and homology searches of the resultant sequences against the DDBJ, EMBL, and GenBank databases revealed that the majority (99%) of the chitinolytic bacteria isolated belonged to the Vibrionaceae. Phylogenetic analysis using a Bayesian approach showed that the α-chitinolytic bacteria belonging to the Vibrionaceae formed a separate cluster from the non-α-chitinolytic bacteria in the Vibrionaceae.Key words: chitinolytic bacteria, 16S rRNA, α-chitin, coastal fish, intestinal bacteria.

scholarly journals Cultivable Microbial Diversity in Speleothems Using MALDI-TOF Spectrometry and DNA Sequencing from Krem Soitan, Krem Lawbah, Krem Mawpun, Khasi Hills, Meghalaya, India

2021 ◽  
Author(s):  
Mudgil Devender ◽  
Dhiraj Paul ◽  
Sushmitha Baskar ◽  
Ramanathan Baskar ◽  
Yogesh S Shouche
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Maldi Tof ◽  
Rrna Gene Sequencing ◽  
Culture Dependent

Abstract This study reports on the culturable microbial communities in caves from the Indian sub-continent. A high bacterial diversity and a greater bacterial taxonomic diversity is reported using MALDI-TOF spectrometry and 16S rRNA gene sequencing. This approach helped to detect a number bacterial strains from the Indian caves. The microbial diversity in the Indian caves is inadequately characterized. The study aims to expand the current understanding of bacterial diversity in the speleothems from Krem Soitan, Krem Lawbah, Krem Mawpun in Khasi Hills, Meghalaya, India. High microbial enumerations were observed on dilute nutrient agar (5.3 × 103 to 8.8 × 105) followed by M9 minimal medium (4 × 104 to 1.7 × 105) and R2A medium (1.0 × 104 to 5.7 × 105). A total of 826 bacterial isolates were selected and preserved for the study. 295 bacterial isolates were identified using MALDI-TOF spectrometry and the isolates which showed no reliable peaks were further identified by 16S rRNA gene sequencing. 91% of the total bacterial diversity was dominated by Proteobacteria and Actinobacteria. The other important phyla detected include the Firmicutes (7.45%), Deinococcus-Thermus (0.33%) and Bacteroidetes (0.67%). At the genus level, Pseudomonas (55%) and Arthrobacter (23%) were ubiquitous followed by Acinetobacter, Bacillus, Brevundimonas, Deinococcus, Flavobacterium, Paenibacillus, Pseudarthrobacter. Multivariate statistical analysis indicated that the bacterial genera formed separate clusters depending on the geochemical constituents in the spring waters suitable for their growth and metabolism. A culture-dependent approach was employed for elucidating the community structure colonizing the speleothems and wall deposits in the caves using MALDI-TOF and 16S rRNA gene sequencing. To the best of our knowledge, there are no previous geomicrobiological investigations in these caves and this study is a pioneering culture dependent study of the microbial community with many cultured isolates.

scholarly journals Bacterial growth in saturated and eutectic solutions of magnesium sulphate and potassium chlorate with relevance to Mars and the ocean worlds

2019 ◽  
Vol 18 (6) ◽  
pp. 502-509 ◽  
Author(s):  
Jonathan M. Wilks ◽  
Fei Chen ◽  
Benton C. Clark ◽  
Mark A. Schneegurt
Keyword(s):  
Microbial Growth ◽  
Freezing Point ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Near Surface ◽  
Iron Sulphate ◽  
High Concentrations ◽  
Rrna Gene Sequencing ◽  
Hygroscopic Salts

AbstractLiquid water on Mars might be created by deliquescence of hygroscopic salts or by permafrost melts, both potentially forming saturated brines. Freezing point depression allows these heavy brines to remain liquid in the near-surface environment for extended periods, perhaps as eutectic solutions, at the lowest temperatures and highest salt concentrations where ices and precipitates do not form. Perchlorate and chlorate salts and iron sulphate form brines with low eutectic temperatures and may persist under Mars near-surface conditions, but are chemically harsh at high concentrations and were expected to be incompatible with life, while brines of common sulphate salts on Mars may be more suitable for microbial growth. Microbial growth in saturated brines also may be relevant beyond Mars, to the oceans of Ceres, Enceladus, Europa and Pluto. We have previously shown strong growth of salinotolerant bacteria in media containing 2M MgSO4 heptahydrate (~50% w/v) at 25°C. Here we extend those observations to bacterial isolates from Basque Lake, BC and Hot Lake, WA, that grow well in saturated MgSO4 medium (67%) at 25°C and in 50% MgSO4 medium at 4°C (56% would be saturated). Psychrotolerant, salinotolerant microbes isolated from Basque Lake soils included Halomonas and Marinococcus, which were identified by 16S rRNA gene sequencing and characterized phenetically. Eutectic liquid medium constituted by 43% MgSO4 at −4°C supported copious growth of these psychrotolerant Halomonas isolates, among others. Bacterial isolates also grew well at the eutectic for K chlorate (3% at −3°C). Survival and growth in eutectic solutions increases the possibility that microbes contaminating spacecraft pose a contamination risk to Mars. The cold brines of sulphate and (per)chlorate salts that may form at times on Mars through deliquescence or permafrost melt have now been demonstrated to be suitable microbial habitats, should appropriate nutrients be available and dormant cells become vegetative.

scholarly journals Culture-Independent Analysis of Bacterial Fuel Contamination Provides Insight into the Level of Concordance with the Standard Industry Practice of Aerobic Cultivation

2011 ◽  
Vol 77 (13) ◽  
pp. 4527-4538 ◽  
Author(s):  
Judith White ◽  
Jack Gilbert ◽  
Graham Hill ◽  
Edward Hill ◽  
Susan M. Huse ◽  
...  
Keyword(s):  
16S Rrna ◽  
Denaturing Gradient Gel Electrophoresis ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Content Type ◽  
Aerobic Culture ◽  
Aerobic Cultivation ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis ◽  
Industry Practice

ABSTRACTBacterial diversity in contaminated fuels has not been systematically investigated using cultivation-independent methods. The fuel industry relies on phenotypic cultivation-based contaminant identification, which may lack accuracy and neglect difficult-to-culture taxa. By the use of industry practice aerobic cultivation, 16S rRNA gene sequencing, and strain genotyping, a collection of 152 unique contaminant isolates from 54 fuel samples was assembled, and a dominance ofPseudomonas(21%),Burkholderia(7%), andBacillus(7%) was demonstrated. Denaturing gradient gel electrophoresis (DGGE) of 15 samples revealedProteobacteriaandFirmicutesto be the most abundant phyla. When 16S rRNA V6 gene pyrosequencing of four selected fuel samples (indicated by “JW”) was performed,Betaproteobacteria(42.8%) andGammaproteobacteria(30.6%) formed the largest proportion of reads; the most abundant genera wereMarinobacter(15.4%; JW57),Achromobacter(41.6%; JW63),Burkholderia(80.7%; JW76), andHalomonas(66.2%; JW78), all of which were also observed by DGGE. However, theClostridia(38.5%) andDeltaproteobacteria(11.1%) identified by pyrosequencing in sample JW57 were not observed by DGGE or aerobic culture. Genotyping revealed three instances where identical strains were found: (i) aPseudomonassp. strain recovered from 2 different diesel fuel tanks at a single industrial site; (ii) aMangroveibactersp. strain isolated from 3 biodiesel tanks at a single refinery site; and (iii) aBurkholderiavietnamiensisstrain present in two unrelated automotive diesel samples. Overall, aerobic cultivation of fuel contaminants recovered isolates broadly representative of the phyla and classes present but lacked accuracy by overrepresenting members of certain groups such asPseudomonas.

scholarly journals Bacterial isolates from bryozoan Pleurocodonellina sp.: Diversity and antimicrobial potential against pathogenic bacteria

2019 ◽  
Vol 20 (9) ◽  
Author(s):  
Meezan Ardhanu Asagabaldan ◽  
Gilles Bedoux ◽  
Nathalie Bourgougnon ◽  
Rhesi Kristiana ◽  
Diah Ayuningrum ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
16S Rrna Gene Sequencing ◽  
Antibacterial Activities ◽  
Multidrug Resistant ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Bacterial Strains ◽  
Associated Bacteria ◽  
Antimicrobial Potential ◽  
Rrna Gene Sequencing

Abstract. Asagabaldan MA, Bedoux G, Bourgougnon N, Kristiana R, Ayuningrum D, Sabdono A, Trianto A, Radjasa OK. 2019. Bacterial isolates from bryozoan Pleurocodonellina sp.: Diversity and antimicrobial potential against pathogenic bacteria. Biodiversitas 20: 2528-2535.  There is an urgent need to discover new compounds with antibacterial activity, which can be developed into lead structures for the treatment of human disease caused by multidrug-resistant (MDR) bacteria. In this study, we focussed on bryozoan-associated bacteria to screen them toward antibacterial activities, since the microbiome of these organisms can still be regarded as under-investigated. Most of the few publications about bryozoan-associated bacteria focused on taxonomy and the potential as producers of antibacterial natural products were neglected. Four specimens of bryozoan Pleurocodonellina sp. were collected from Teluk Awur, Jepara in Java Sea, Indonesia. Therefrom, 56 bacterial strains were isolated, and 17 displayed antibacterial activities against MDR bacteria Pseudomonas aruginosa, Klebsiella pneumoniae, Acinetobacter baumannii, Enterobacter cloacae, and methicillin-resistant Staphylococcus aureus (MRSA). Taxonomic identification of the bacteria by 16S rRNA gene sequencing revealed them belonging to the genera Virgibacillus, Pseudoalteromonas, Halomonas, and Bacillus. Most interestingly, the genus Virgibacillus was dominantly obtained from the Pleurocodonellina sp. specimens, i.e., 12 active isolates. Nevertheless, the best activities against MDR bacteria (both Gram-positive and Gram-negative) were contributed to isolates showing >99% identity to Pseudoalteromonas. The results further suggest adding the genus Virgibacillus as bacteria associated with bryozoan, since to the best of our knowledge there were no reports of this genus isolated from bryozoan.

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