scholarly journals The Root Mycobiota of Betula aetnensis Raf., an Endemic Tree Species Colonizing the Lavas of Mt. Etna (Italy)

Forests ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1624
Author(s):  
Emilio Badalamenti ◽  
Valentina Catania ◽  
Serena Sofia ◽  
Maria Teresa Sardina ◽  
Giovanna Sala ◽  
...  
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Natural Habitat ◽  
Intergenic Spacer ◽  
Illumina Miseq ◽  
Resistance Mechanisms ◽  
Mount Etna ◽  
Dominant Component ◽  
Mt Etna ◽  
Gradient Gel Electrophoresis ◽  
High Conservation

Betula aetnensis is an endemic tree of high conservation value, which thrives on the nutrient-poor volcanic soils of Mount Etna. Since plant–microbe interactions could play a crucial role in plant growth, resource uptake, and resistance to abiotic stresses, we aimed to characterize the root and rhizosphere microbial communities. Individuals from natural habitat (NAT) and forest nursery (NURS) were surveyed through microscopy observations and molecular tools: bacterial and fungal automated ribosomal intergenic spacer analysis (ARISA), fungal denaturing gradient gel electrophoresis (DGGE). B. aetnensis was found to be simultaneously colonized by arbuscular (AM), ectomycorrhizal (ECM), ericoid (ERM) fungi, and dark septate endophytes (DSE). A high diversity of the bacterial community was observed whilst the root fungal assemblage of NAT plants was richer than that of NURS. Root and rhizosphere fungal communities from NAT plants were characterized by Illumina MiSeq sequencing. Most of the identified sequences were affiliated to Helotiales, Pezizales, and Malasseziales. Ascomycota and Basidiomycota dominated roots and rhizosphere but differed in community structure and composition. ECM in the roots mainly belonged to Tylospora and Leccinum, while Rhizopogon was abundant in the rhizosphere. The Helotiales, including ERM (mostly Oidiodendron) and DSE (mostly Phialocephala), appeared the dominant component of the fungal community. B. aetnensis harbors an extraordinarily wide array of root-associated soil microorganisms, which are likely to be involved in the adaptation and resistance mechanisms to the extreme environmental conditions in volcano Etna. We argue that nursery-produced seedlings could lack the necessary microbiota for growth and development in natural conditions.

scholarly journals Quantitative Tracing, by Taq Nuclease Assays, of a Synechococcus Ecotype in a Highly Diversified Natural Population

2002 ◽  
Vol 68 (9) ◽  
pp. 4486-4494 ◽  
Author(s):  
Sven Becker ◽  
Michael Fahrbach ◽  
Peter Böger ◽  
Anneliese Ernst
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Intergenic Spacer ◽  
Microscopic Analysis ◽  
Growth Period ◽  
Culture Collection ◽  
Detection Methods ◽  
Epifluorescence Microscopy ◽  
Lake Constance ◽  
Gradient Gel Electrophoresis ◽  
Pelagic Habitat

ABSTRACT Quantitative Taq nuclease assays (TNAs) (TaqMan PCR), nested PCR in combination with denaturing gradient gel electrophoresis (DGGE), and epifluorescence microscopy were used to analyze the autotrophic picoplankton (APP) of Lake Constance. Microscopic analysis revealed dominance of phycoerythrin (PE)-rich Synechococcus spp. in the pelagic zone of this lake. Cells passing a 3-μm-pore-size filter were collected during the growth period of the years 1999 and 2000. The diversity of PE-rich Synechococcus spp. was examined using DGGE to analyze GC-clamped amplicons of a noncoding section of the 16S-23S intergenic spacer in the ribosomal operon. In both years, genotypes represented by three closely related PE-rich Synechococcus strains of our culture collection dominated the population, while other isolates were traced sporadically or were not detected in their original habitat by this method. For TNAs, primer-probe combinations for two taxonomic levels were used, one to quantify genomes of all known Synechococcus-type cyanobacteria in the APP of Lake Constance and one to enumerate genomes of a single ecotype represented by the PE-rich isolate Synechococcus sp. strain BO 8807. During the growth period, genome numbers of known Synechococcus spp. varied by 2 orders of magnitude (2.9 × 103 to 3.1 × 105 genomes per ml). The ecotype Synechococcus sp. strain BO 8807 was detected in every sample at concentrations between 1.6 × 101 and 1.3 × 104 genomes per ml, contributing 0.02 to 5.7% of the quantified cyanobacterial picoplankton. Although the quantitative approach taken in this study has disclosed several shortcomings in the sampling and detection methods, this study demonstrated for the first time the extensive internal dynamics that lie beneath the seemingly arbitrary variations of a population of microbial photoautotrophs in the pelagic habitat.

Source tracking ofEscherichia coliby 16S–23S intergenic spacer region denaturing gradient gel electrophoresis (DGGE) of therrnBribosomal operon

2007 ◽  
Vol 53 (10) ◽  
pp. 1174-1184 ◽  
Author(s):  
Thomas V. D’Elia ◽  
Chester R. Cooper ◽  
Carl G. Johnston
Keyword(s):  
Escherichia Coli ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Intergenic Spacer ◽  
Source Tracking ◽  
Combined Sewer Overflow ◽  
Intergenic Spacer Region ◽  
E Coli ◽  
Combined Sewer ◽  
Gradient Gel Electrophoresis

This research validates a novel approach for source tracking based on denaturing gradient gel electrophoresis (DGGE) analysis of DNA extracted from Escherichia coli isolates. Escherichia coli from different animal sources and from river samples upstream from, at, and downstream of a combined sewer overflow were subjected to DGGE to determine sequence variations within the 16S–23S intergenic spacer region (ISR) of the rrnB ribosomal operon. The ISR was analyzed to determine if E. coli isolates from various animal sources could be differentiated from each other. DNA isolated from the E. coli animal sources was PCR amplified to isolate the rrnB operon. To prevent amplification of all 7 E. coli ribosomal operons by PCR amplification using universal primers, sequence-specific primers were utilized for the rrnB operon. Another primer set was then used to prepare samples of the 16S–23S ISR for DGGE. Comparison of PCR–DGGE results between human and animal sources revealed differences in the distribution and frequency of the DGGE bands produced. Human and Canada Goose isolates had the most unique distribution patterns and the highest percent of unique isolates and were grouped separately from all other animal sources. Method validation suggests that there are enough host specificity and genetic differences for use in the field. Field results at and around a combined sewer overflow indicate that this method can be used for microbial source tracking.

scholarly journals Microbiota Dynamics Associated with Environmental Conditions and Potential Roles of Cellulolytic Communities in Traditional Chinese Cereal Starter Solid-State Fermentation

2015 ◽  
Vol 81 (15) ◽  
pp. 5144-5156 ◽  
Author(s):  
Pan Li ◽  
Hebin Liang ◽  
Wei-Tie Lin ◽  
Feng Feng ◽  
Lixin Luo
Keyword(s):  
Solid State ◽  
Environmental Conditions ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Incubation Temperature ◽  
Illumina Miseq ◽  
Miseq Sequencing ◽  
Microbial Dynamics ◽  
Content Type ◽  
Gradient Gel Electrophoresis ◽  
Clone Library Construction

ABSTRACTTraditional Chinese solid-state fermented cereal starters contain highly complex microbial communities and enzymes. Very little is known, however, about the microbial dynamics related to environmental conditions, and cellulolytic communities have never been proposed to exist during cereal starter fermentation. In this study, we performed Illumina MiSeq sequencing combined with PCR-denaturing gradient gel electrophoresis to investigate microbiota, coupled with clone library construction to trace cellulolytic communities in both fermentation stages. A succession of microbial assemblages was observed during the fermentation of starters.LactobacillalesandSaccharomycetalesdominated the initial stages, with a continuous decline in relative abundance. However, thermotolerant and drought-resistantBacillales,Eurotiales, andMucoraleswere considerably accelerated during the heating stages, and these organisms dominated until the end of fermentation.Enterobacterialeswere consistently ubiquitous throughout the process. For the cellulolytic communities, only the generaSanguibacter,Beutenbergia,Agrobacterium, andErwiniadominated the initial fermentation stages. In contrast, stages at high incubation temperature induced the appearance and dominance ofBacillus,Aspergillus, andMucor. The enzymatic dynamics of amylase and glucoamylase also showed a similar trend, with the activities clearly increased in the first 7 days and subsequently decreased until the end of fermentation. Furthermore, β-glucosidase activity continuously and significantly increased during the fermentation process. Evidently, cellulolytic potential can adapt to environmental conditions by changes in the community structure during the fermentation of starters.

scholarly journals Examination of faecal Bifidobacterium populations in breast- and formula-fed infants during the first 18 months of life

Microbiology ◽  
2010 ◽  
Vol 156 (11) ◽  
pp. 3329-3341 ◽  
Author(s):  
Laure C. Roger ◽  
Adele Costabile ◽  
Diane T. Holland ◽  
Lesley Hoyles ◽  
Anne L. McCartney
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Bifidobacterium Longum ◽  
Intergenic Spacer ◽  
Bifidobacterium Bifidum ◽  
Faecal Microbiota ◽  
Ribosomal Intergenic Spacer ◽  
Infant Formulae ◽  
Gradient Gel Electrophoresis ◽  
Breast Fed ◽  
Milk Feeding

Bifidobacteria in the infant faecal microbiota have been the focus of much interest, especially during the exclusive milk-feeding period and in relation to the fortification of infant formulae to better mimic breast milk. However, longitudinal studies examining the diversity and dynamics of the Bifidobacterium population of infants are lacking, particularly in relation to the effects of weaning. Using a polyphasic strategy, the Bifidobacterium populations of breast- and formula-fed infants were examined during the first 18 months of life. Bifidobacterium-specific denaturing gradient gel electrophoresis demonstrated that breast-fed infants harboured greater diversity than formula-fed infants and the diversity of the infants' Bifidobacterium populations increased with weaning. Twenty-seven distinctive banding profiles were observed from ∼1100 infant isolates using ribosomal intergenic spacer analysis, 14 biotypes of which were confirmed to be members of the genus Bifidobacterium. Two profiles (H, Bifidobacterium longum subsp. infantis; and I, Bifidobacterium bifidum) were common culturable biotypes, seen in 9/10 infants, while profile E (Bifidobacterium breve) was common among breast-fed infants. Overall, inter- and intra-individual differences were observed in the Bifidobacterium populations of infants between 1 and 18 months of age, although weaning was associated with increased diversity of the infant Bifidobacterium populations. Breast-fed infants generally harboured a more complex Bifidobacterium microbiota than formula-fed infants.

Allelopathic and Medicinal plant. 26. Millettia speciosa

2020 ◽  
Vol 51 (2) ◽  
pp. 125-146
Author(s):  
Nasiruddin Nasiruddin ◽  
Yu Zhangxin ◽  
Ting Zhao Chen Guangying ◽  
Minghui Ji
Keyword(s):  
Community Structure ◽  
Medicinal Plant ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Wiener Index ◽  
Pseudomonas Spp ◽  
Evenness Index ◽  
Gradient Gel Electrophoresis ◽  
Rhizosphere Pseudomonas

We grew cucumber in pots in greenhouse for 9-successive cropping cycles and analyzed the rhizosphere Pseudomonas spp. community structure and abundance by PCR-denaturing gradient gel electrophoresis and quantitative PCR. Results showed that continuous monocropping changed the cucumber rhizosphere Pseudomonas spp. community. The number of DGGE bands, Shannon-Wiener index and Evenness index decreased during the 3rd cropping and thereafter, increased up to the 7th cropping, however, however, afterwards they decreased again. The abundance of Pseudomonas spp. increased up to the 5th successive cropping and then decreased gradually. These findings indicated that the structure and abundance of Pseudomonas spp. community changed with long-term cucumber monocropping, which might be linked to soil sickness caused by its continuous monocropping.

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