scholarly journals Taxonomic structure of tissue endophytic bacterial microbiome in clonal apple rootstock grown on sod-podzolic soils with variant properties

2021 ◽  
pp. 36-44
Author(s):  
V. V. Bobkova ◽  
S. N. Konovalov ◽  
M. T. Upadyshev
Keyword(s):  
Diversity Indices ◽  
Shannon Index ◽  
Taxonomic Structure ◽  
Apple Rootstock ◽  
Apple Rootstocks ◽  
Bacterial Phyla ◽  
Podzolic Soils ◽  
Bacterial Microbiome ◽  
Callus Tissues

The taxonomic structure of tissue endophytic bacterial microbiome was comparatively studied in microplants (undifferentiated explant callus tissues, passage 25) and 5-year clonal apple rootstocks 57-490 and 54-118 cultured from corresponding tissues (passage 1) on sod-podzolic soils with variant granulometry, chemical, physical and physicochemical properties. Proteobacteria (91.6 %) predominated in vitro tissues among other endophytic bacterial phyla in rootstock 57-490, while Proteobacteria (52.5 %) and Firmicutes (47.4 %) — in rootstock 54-118. The endophytic Firmicutes ratio vs. in vitro tissues decreases (0.7-2.0 %) in roots and more severely (0-0.2 %) in leaves. Endophytic Actinobacteriota are revealed in 11.7 % in roots of the study rootstock in heavy loam soil, whilst in medium loam their ratio drops to 2.74.1 % in roots and 0.1-0.2 % in leaves. The phylogenetic diversity indices estimation for main endophytic bacterial phyla in apple rootstock tissue recovers their essentially lower diversity and evenness in culture endosphere (Shannon index 0.42-1.00) vs. open soil roots (1.34-2.08). The leaves Shannon index is typically low (0.06-0.13) indicating poor diversity and evenness of the main endophytic bacterial phyla.

scholarly journals Phylogenetic diversity of the endophytic bacterial component of the microbiome of apple clonal rootstocks during in vitro reproduction and cultivation under various agroecological conditions

2021 ◽  
Vol 34 ◽  
pp. 04009
Author(s):  
Veronika Bobkova ◽  
Sergey Konovalov ◽  
Mikhail Upadyshev
Keyword(s):  
Endophytic Bacteria ◽  
Phylogenetic Diversity ◽  
Granulometric Composition ◽  
Shannon Index ◽  
Relative Content ◽  
Plant Tissues ◽  
Apple Rootstock ◽  
Loamy Soil ◽  
Podzolic Soils

The phylogenetic diversity of the endophytic bacterial component of the clonal apple rootstock microbiome 57-490 and 54-118 was studied for microplants and 5-year-old plants grown from the same tissue culture and growing on sod-podzolic soils of different granulometric composition with different chemical, physicochemical and physical properties. Proteobacteria (91.6%) in rootstock 57-490, Proteobacteria (52.5%) and Firmicutes (47.4%) in rootstock 54-118 are the predominant phylum of endophytic bacteria in apple rootstock plant tissues in vitro culture. The relative amount of phylum Firmicutes endophytic bacteria, in comparison with in vitro culture, decreases in the roots to 0.7-2.0%, and even more significantly in the leaves (to 0-0.2%). At cultivation on heavy loamy soil, endophytic bacteria belonging to the phylum Actinobacteriota (11.7%) are found in the studied rootstock roots, the relative content of which, when grown on medium loamy soil, in the roots decreases to 2.7-4.1%, in the leaves – to 0,1-0.2%. The data show that in the endosphere of the culture in vitro, the diversity and uniformity of the community of endophytic bacteria is significantly lower (Shannon index 0.42-1.00) than in the roots of rootstocks grown in the outdoor growing (1.34-2.08). For leaves, the Shannon index is characterized by the lowest values (0.06-0.13).

scholarly journals TAXONOMIC STRUCTURE OF PROKARYOTIC COMMUNITIES IN SOILS OF DIFFERENT BIOCLIMATIC ZONES

2018 ◽  
pp. 125-153 ◽  
Author(s):  
I. A. Tikhonovich ◽  
T. I. Chernov ◽  
A. D. Zhelezova ◽  
A. K. Tkhakakhova ◽  
E. E. Andronov ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Profile Analysis ◽  
Chestnut Soil ◽  
Diversity Indices ◽  
Taxonomic Structure ◽  
Typical Chernozem ◽  
Bacterial Phyla ◽  
Dry Steppe ◽  
Full Profile ◽  
The Difference

Using high-throughput sequencing, we performed a full-profile analysis of the taxonomic structure and diversity of prokaryotic communities of zonal soil series: sod-podzolic, dark gray, typical chernozem, brown soil, meadow-chestnut soil and solonets. Phyla Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, Planctomycetes, Proteobacteria and Verrucomicrobia formed up to 95% of prokaryotic communities in all studied soil horizons. Phyla Proteobacteria and Actinobacteria and archaeal phylum Thaumarchaeota dominated in all soils. We revealed the trends of changes in the representation of bacterial phyla in the soils of the zonal range from taiga to dry-steppe: a decrease of Acidobacteria and an increase of Actinobacteria in the upper horizons. The diversity indices of the prokaryotic communities of different genetic horizons of the studied soils were evaluated. In all soils, a decrease in diversity indices with the depth of the horizon was revealed. In all soils, a decrease in diversity indices with depth of the horizon was found, with a rare and slight increase in some lower horizons: structural metamorphic (BM), textural (BT) or accumulative carbonate (BCA) horizons. When examining the prokaryotic communities of soils with different genesis, no determining influence of pH and organic matter contents on the diversity indices was found. Differences in the taxonomic structure and diversity of prokaryotic communities of soils of different bioclimatic zones were presented due to a combination of factors: the difference in chemical and physical properties of soils, as well as in water and temperature conditions.

scholarly journals Micropropagation of the new apple rootstock ‘G. 814’

2017 ◽  
Vol 47 (6) ◽  
Author(s):  
Aline Meneguzzi ◽  
Mayra Juline Gonçalves ◽  
Samila Silva Camargo ◽  
Fernanda Grimaldi ◽  
Gabriela Candido Weber ◽  
...  
Keyword(s):  
Tissue Culture ◽  
Vegetative Propagation ◽  
In Vitro Propagation ◽  
Genetic Material ◽  
Apple Rootstock ◽  
Apple Rootstocks ◽  
Breeding Programs ◽  
Soil Pests ◽  
Great Yield

ABSTRACT: International breeding programs launched new genetic material of apple rootstocks that in addition to precocity and great yield are resistant to major diseases and soil pests encountered in the largest apple producing regions in Brazil. Given this, there is a necessity for vegetative propagation of these materials for study and possible replacement of existing rootstocks. The objective was to adapt a micropropagation protocol for new apple rootstock ‘G. 814’. In the multiplication phase were evaluated BAP concentrations: 0; 0.5; 1; 2 and 4mg L-1 and in the rooting phase were evaluated IBA concentrations: 0; 0.25; 0.50; 1; 1.5 and 2.5mg L-1. These new results demonstrated that this new rootstock selection can be propagated with this tissue culture adapted protocol. For the successful in vitro propagation of apple rootstock ‘G. 814’ it is indicated the use of 1mg L-1 BAP at multiplication phase and 1.5mg L-1 IBA at rooting phase.

scholarly journals Fungal and Bacterial Microbiome Associated with the Rhizosphere of Native Plants from the Atacama Desert

2020 ◽  
Vol 8 (2) ◽  
pp. 209 ◽  
Author(s):  
Alejandra Fuentes ◽  
Héctor Herrera ◽  
Trevor C. Charles ◽  
Cesar Arriagada
Keyword(s):  
Bacterial Communities ◽  
Native Plants ◽  
Atacama Desert ◽  
Illumina Miseq ◽  
Shannon Index ◽  
Linear Discriminant ◽  
Bacterial Phyla ◽  
Rhizosphere Microbiome ◽  
Bacterial Microbiome ◽  
Solanum Chilense

The rhizosphere microbiome is key in survival, development, and stress tolerance in plants. Salinity, drought, and extreme temperatures are frequent events in the Atacama Desert, considered the driest in the world. However, little information of the rhizosphere microbiome and its possible contribution to the adaptation and tolerance of plants that inhabit the desert is available. We used a high-throughput Illumina MiSeq sequencing approach to explore the composition, diversity, and functions of fungal and bacterial communities of the rhizosphere of Baccharis scandens and Solanum chilense native plants from the Atacama Desert. Our results showed that the fungal phyla Ascomycota and Basidiomycota and the bacterial phyla Actinobacteria and Proteobacteria were the dominant taxa in the rhizosphere of both plants. The linear discriminant analysis (LDA) effect size (LefSe) of the rhizosphere communities associated with B. scandens showed the genera Penicillium and Arthrobacter were the preferential taxa, whereas the genera Oidiodendron and Nitrospirae was the preferential taxa in S. chilense. Both plant showed similar diversity, richness, and abundance according to Shannon index, observed OTUs, and evenness. Our results indicate that there are no significant differences (p = 0.1) between the fungal and bacterial communities of both plants, however through LefSe, we find taxa associated with each plant species and the PCoA shows a separation between the samples of each species. This study provides knowledge to relate the assembly of the microbiome to the adaptability to drought stress in desert plants.

scholarly journals Assessment of fire blight resistance in apple clonal rootstocks using molecular markers

2021 ◽  
Vol 181 (4) ◽  
pp. 185-191
Author(s):  
I. N. Shamshin ◽  
M. V. Maslova ◽  
N. V. Drenova ◽  
M. L. Dubrovsky ◽  
O. V. Parusova
Keyword(s):  
Microsatellite Marker ◽  
Fire Blight ◽  
Erwinia Amylovora ◽  
Leaf Explants ◽  
The Other ◽  
Scar Markers ◽  
Apple Rootstock ◽  
Apple Rootstocks ◽  
Main Components

Background. Clonal apple rootstocks are one of the main components of intensive gardening. The degree of rootstock damage by fire blight affects the resistance of the variety–rootstock combination. The paper presents a study on marking quantitative trait loci (QTL) of resistance to fire blight Erwinia amylovora in clonal apple rootstock.Materials and methods. A collection of 20 rootstock forms was analyzed. For the study, SCAR markers GE-8019, AE10-375 and microsatellite marker CH-F7-FB1 were used.Results. Polymorphism was observed for all three markers, and their various combinations in one genotype were revealed. It was previously noted that genotypes that carry all three markers were more resistant than those that lack them. The presence of all three markers was observed only in forms 62-396 (В10), 16-1 and 2-9-102. The other genotypes did not have the GE8019 marker. The AE10-375 marker was identified in eight clonal rootstocks. Microsatellite marker CH-F7-FB1 was present in all tested rootstocks. However, polymorphism was detected there. Most genotypes had a 174 bp fragment, but a 210 bp fragment was identified in two of the 20 forms. Clonal rootstock 70-20-21 proved heterozygous for this marker. The analyzed collection also included samples that had only the microsatellite marker: G16, Malysh Budagovskogo, Paradizka Budagovskogo (B9), 54-118 (В118), 57-491, 70-20-20 (В119), 70-20-21, 71-7-22, 76-3-6, 83-1-15, 87-7-12, and 2-12-10. The study of rootstock forms on the basis of resistance to metabolites of the fire blight pathogen was carried out under laboratory conditions using the E. amylovora culture filtrate in vitro on leaf explants. Most of the studied genotypes had different combinations of markers. However, the experiments showed that forms 62-396 and 14-1 with two out of three markers (AE10-375 and CH-F7-FB1) phenotypically manifested the trait of resistance to metabolites of E. amylovora. 

In Vitro Shoot Regeneration from Callus Derived from Marubakaido Apple Rootstock under Different Aluminium Concentrations

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 460e-460 ◽  
Author(s):  
Marisa F. de Oliveira ◽  
Gerson R. de L. Fortes ◽  
João B. da Silva
Keyword(s):  
Shoot Regeneration ◽  
Dichlorophenoxyacetic Acid ◽  
Apple Rootstock ◽  
Under Five ◽  
Significant Difference ◽  
Previously Treated ◽  
2,4 Dichlorophenoxyacetic Acid ◽  
In Vitro Shoot Regeneration

The aim of this work was to evaluate the organogenesis of Marubakaido apple rootstock under different aluminium concentratons. The explants were calli derived from apple internodes treated with either 2,4-dichlorophenoxyacetic acid or pichloram at 0.5 and 1.0 μM and under five different aluminium concentrations (0, 5, 10, 15, 20 mg/L). These calli were then treated with aluminium at 0, 5, 10, 15, and 20 mg/L. It was observed shoot regeneration only for those calli previously treated with pichloram. There were no significant difference among the aluminium concentrations.

scholarly journals Impact of sulfamethoxazole on a riverine microbiome

2021 ◽  
Author(s):  
Chiara Borsetto ◽  
Sebastien Raguideau ◽  
Emma R Travis ◽  
Dae-Wi Kim ◽  
Do-Hoon Lee ◽  
...  
Keyword(s):  
River Flow ◽  
Wastewater Treatment Plants ◽  
Antibiotic Resistance Genes ◽  
Resistant Bacteria ◽  
Water Fraction ◽  
Riverine Ecosystems ◽  
Short Term Exposure ◽  
Bacterial Microbiome ◽  
The Impact

The continued emergence of bacterial pathogens presenting antimicrobial resistance is widely recognised as a global health threat and recent attention focused on potential environmental reservoirs of antibiotic resistance genes (ARGs). Freshwater environments such as rivers represent a potential hotspot for ARGs and antibiotic resistant bacteria as they are receiving systems for effluent discharges from wastewater treatment plants (WWTPs). Effluent also contains low levels of different antimicrobials including antibiotics and biocides. Sulfonamides are antibacterial chemicals widely used in clinical, veterinary and agricultural settings and are frequently detected in sewage sludge and manure in addition to riverine ecosystems. The impact of such exposure on ARG prevalence and diversity is unknown, so the aim of this study was to investigate the release of a sub-lethal concentration of the sulfonamide compound sulfamethoxazole (SMX) on the river bacterial microbiome using a flume system. This system was a semi-natural in vitro flume using river water (30 L) and sediment with circulation to mimic river flow. A combination of 'omics' approaches were conducted to study the impact of SMX exposure on the microbiomes within the flumes. Metagenomic analysis showed that the addition of low concentrations of SMX (<4 μg L-1) had a limited effect on the bacterial resistome in the water fraction only, with no impact observed in the sediment. Metaproteomics did not show differences in ARGs expression with SMX exposure in water. Overall, the river bacterial community was resilient to short term exposure to sub-lethal concentrations of SMX which mimics the exposure such communities experience downstream of WWTPs throughout the year.

scholarly journals Isolation of furanocoumarins from Pastinaca sativa L. callus culture

2014 ◽  
Vol 69 (3) ◽  
pp. 193-195 ◽  
Author(s):  
Halina Ekiert ◽  
Wanda Kisiel
Keyword(s):  
Secondary Metabolites ◽  
Callus Culture ◽  
Spectral Methods ◽  
Solid Medium ◽  
Intact Plant ◽  
Pastinaca Sativa ◽  
First Report ◽  
Callus Tissues ◽  
First Time

Four furanocoumarins: bergapten, xanthotoxin, isopimpinellin (linear furanocoumarins) and sphondin (angular furanocoumarin) were isolated for the first time from callus tissues of <em>Pastinaca sativa</em> L.(<em>Apiaceae</em>) cultured in vitro on solid medium. The compounds were identified using spectral methods. They are well-known secondary metabolites of the intact plant. This is the first report on the isolation of sphondin from in vitro plant cultures.

scholarly journals DYNAMICS OF FRUIT FLIES POPULATIONS IN TWO MANGO PRODUCTION ZONES (KORHOGO AND FERKÉ) IN NORTHERN CÔTE D’IVOIRE

2019 ◽  
Vol 7 (7) ◽  
pp. 256-264
Author(s):  
Minhibo Magloire Yves ◽  
Akpesse Akpa Alexandre Moïse ◽  
Coulibaly Tenon ◽  
Koua K Hervé ◽  
Coulibaly Adama
Keyword(s):  
Cote D'ivoire ◽  
Côte D’Ivoire ◽  
Diversity Indices ◽  
Fruit Flies ◽  
Shannon Index ◽  
Bactrocera Dorsalis ◽  
Cote D’Ivoire ◽  
Côte D'ivoire ◽  
Set Up ◽  
Study Sites

Fruit flies are a major constraint to the production and export of mangoes by causing the rot of mangoes. The objective of this work is to follow the fluctuation of population of flies in the northern part of Côte d'Ivoire between May 2015 and October 2016. A network of trapping flies using food baits (the Torula and Ceratrap) and sexual attractants (Methyl Eugenol and Trimedlure) were set up in Korhogo and Ferké mango orchards with the forest Diabaté Kamonon and the forest Petit Clerc as reference area. During trapping, 11 species of fruit flies were identified at all study sites. Among these species, Bactrocera dorsalis and Ceratitis cosyra, were the most abundant in the area. In general, diversity indices were low. The Ferké’s Forest has the highest Shannon index (H = 1.20). This index was higher than the index found in Ferke's orchards (0.9398). At Korhogo the Shannon index in orchards (H = 0.84) is higher than in the forest (H = 0.41). It has been observed that the genus Bactrocera swarmed on mango orchards when precipitation was plentiful. While the genus Cerartitis only appeared when precipitation was low. In addition, knowledge of the ecology and fluctuation of fruit flies, will allow to develop a site monitoring device through a trapping system with sexual and food attractants.

scholarly journals Dw2, a New Dwarfing Locus in Apple Rootstocks and Its Relationship to Induction of Early Bearing in Apple Scions

2014 ◽  
Vol 139 (2) ◽  
pp. 87-98 ◽  
Author(s):  
Gennaro Fazio ◽  
Yizhen Wan ◽  
Dariusz Kviklys ◽  
Leticia Romero ◽  
Richard Adams ◽  
...  
Keyword(s):  
Genetic Map ◽  
Production Systems ◽  
Breeding Population ◽  
Breeding Strategy ◽  
Nucleotide Polymorphisms ◽  
Apple Rootstock ◽  
Apple Rootstocks ◽  
Yield Data ◽  
Trait Locus ◽  
Rootstock Breeding

The ability of certain apple rootstocks to dwarf their scions has been known for centuries and their use revolutionized apple (Malus ×domestica) production systems. In this investigation, several apple rootstock breeding populations, planted in multiple replicated field and pot experiments, were used to ascertain the degree of dwarfing when grafted with multiple scions. A previous genetic map of a breeding population derived from parents ‘Ottawa 3’ (O.3) and ‘Robusta 5’ (R5) was used for quantitative trait locus (QTL) analysis of traits related to scion vigor suppression, induction of early bearing, and other tree size measurements on own-rooted and grafted trees. The analysis confirmed a previously reported QTL that imparts vigor control [Dw1, log of odds (LOD) = 7.2] on linkage group (LG) 5 and a new QTL named Dw2 (LOD = 6.4) on LG11 that has a similar effect on vigor. The data from this population were used to study the interaction of these two loci. To validate these findings, a new genetic map comprised of 1841 single-nucleotide polymorphisms was constructed from a cross of the dwarfing, precocious rootstocks ‘Geneva 935’ (G.935) and ‘Budagovsky 9’ (B.9), resulting in the confirmation and modeling of the effect of Dw1 and Dw2 on vigor control of apple scions. Flower density and fruit yield data allowed the identification of genetic factors Eb1 (LOD = 7.1) and Eb2 (LOD = 7.6) that cause early bearing of scions, roughly colocated with the dwarfing factors. The major QTL for mean number of fruit produced per tree colocated with Dw2 (LOD = 7.0) and a minor QTL was located on LG16 (LOD = 3.5). These findings will aid the development of a marker-assisted breeding strategy, and the discovery of additional sources for dwarfing and predictive modeling of new apple rootstocks in the Geneva® apple rootstock breeding program.

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