Microbial communities in roots ofPinus sylvestrisseedlings with damping-off symptoms in two forest nurseries as determined by ITS1/2 rDNA sequencing

2009 ◽  
Vol 39 (4) ◽  
pp. 239-248 ◽  
Author(s):  
H. Kwaśna ◽  
G. L. Bateman
Keyword(s):  
Microbial Communities ◽  
Damping Off ◽  
Rdna Sequencing ◽  
Forest Nurseries

scholarly journals Biological Control of Pythium Damping –off in Seedlings with Streptomyces Sp.

2019 ◽  
Vol 8 (4) ◽  
pp. 8035-8039
Keyword(s):  
Biological Control ◽  
Antifungal Activity ◽  
Research Work ◽  
Pythium Aphanidermatum ◽  
Dual Culture ◽  
Damping Off ◽  
Zone Of Inhibition ◽  
Streptomyces Sp ◽  
Rdna Sequencing ◽  
Forest Nurseries

Damping-off is one of the severe diseases caused by soil-borne pathogens notably Pythium sp. the causative agent of this infection in raising tree saplings in forest nurseries. Biological control is an eco-friendly approach in disease management compared to chemical fungicides which in turn affects the soil environment. Biocontrol of Pythium sp. has been emphasized in vegetable nurseries than forest nurseries. The present research work is focused on identification of effective antagonistic organism from forest nursery soils against Pythium aphanidermatum. Bacteria were isolated from various forest soils collected from Boluvampati, Sirumugai and Mettupalayam forest nurseries in Coimbatore district and soil samples were screened for antifungal activity against Pythium aphanidermatum by dual culture technique. Among 245 bacterial isolates, one isolate KUMB1.1 exhibited clear zone of inhibition of 1cm and it was identified by 16S rDNA sequencing as Streptomyces sp. Solvent extraction was performed to isolate an active compound using ethyl acetate, dichloromethane, n-butanol, hexane and chloroform in the ratio 1:1. The antifungal activity of compound was performed by well plate method against Pythium sp. and nbutanol extract exhibited zone of inhibition. The antifungal activity of Streptomyces sp. was tested in a model plant Solanum lycopersicum (Tomato) seeds raised in Pythium aphanidermatum infested soils in seed trays under in vitro conditions. Preemergence and post-emergence disease incidences were observed, and the results exhibited promising efficacy of Streptomyces sp. against the fungal pathogen Pythium aphanidermatum. Seedbed study was carried out in Gmelina arborea seeds, where the seeds are treated with Streptomyces culture broth. In which seed treatment shows 43% increase in germination compared with control.

scholarly journals Pathogenicity and Virulence of Pythium Species Obtained from Forest Nursery Soils on Douglas-Fir Seedlings

Plant Disease ◽  
2013 ◽  
Vol 97 (6) ◽  
pp. 744-748 ◽  
Author(s):  
Jerry E. Weiland ◽  
Bryan R. Beck ◽  
Anne Davis
Keyword(s):  
Pseudotsuga Menziesii ◽  
Seedling Survival ◽  
The United States ◽  
Douglas Fir ◽  
Tree Seedlings ◽  
Pythium Species ◽  
Forest Nursery ◽  
Damping Off ◽  
Greenhouse Study ◽  
Forest Nurseries

Pythium species are common soilborne oomycetes that occur in forest nursery soils throughout the United States. Numerous species have been described from nursery soils. However, with the exception of P. aphanidermatum, P. irregulare, P. sylvaticum, and P. ultimum, little is known about the potential for other Pythium species found in nursery soils to cause damping-off of tree seedlings. A greenhouse study was conducted to evaluate the pathogenicity and virulence of 44 Pythium isolates representing 16 species that were originally recovered from soil at three forest nurseries in Washington and Oregon. Seeds of Douglas-fir (Pseudotsuga menziesii) were planted into soil infested with each of the isolates. Seedling survival, the number of surviving seedlings with necrotic root lesions, and taproot length were evaluated 4 weeks later. Responses of Douglas-fir to inoculation varied significantly depending on Pythium species and isolate. Eight species (P. dissotocum, P. irregulare, P. aff. macrosporum, P. mamillatum, P. aff. oopapillum, P. rostratifingens, P. sylvaticum, and P. ultimum var. ultimum) significantly reduced the number of surviving seedlings compared to the noninoculated treatment. However, all Pythium species caused a greater percentage of seedlings to develop root lesions (total mean 40%) than was observed from noninoculated seedlings (17%). Taproot length varied little among Pythium treatments and was not a useful character for evaluating pathogenicity. Results confirm the ability of P. irregulare, P. mamillatum, and P. ultimum var. ultimum to cause damping-off of Douglas-fir seedlings, and are indicative that other species such as P. dissotocum, P. aff. macrosporum, P. aff. oopapillum, P. rostratifingens, and P. sylvaticum may also be responsible for seedling loss.

scholarly journals Cave Drip Water-Related Samples as a Natural Environment for Aromatic Hydrocarbon-Degrading Bacteria

2019 ◽  
Vol 7 (2) ◽  
pp. 33 ◽  
Author(s):  
Eric Marques ◽  
Gislaine Silva ◽  
João Dias ◽  
Eduardo Gross ◽  
Moara Costa ◽  
...  
Keyword(s):  
Aromatic Hydrocarbon ◽  
Microbial Communities ◽  
16S Rdna ◽  
Aromatic Compounds ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Amplicon Sequencing ◽  
Drip Water ◽  
Rdna Sequencing ◽  
Degrading Bacteria ◽  
Cave Drip Water

Restricted contact with the external environment has allowed the development of microbial communities adapted to the oligotrophy of caves. However, nutrients can be transported to caves by drip water and affect the microbial communities inside the cave. To evaluate the influence of aromatic compounds carried by drip water on the microbial community, two limestone caves were selected in Brazil. Drip-water-saturated and unsaturated sediment, and dripping water itself, were collected from each cave and bacterial 16S rDNA amplicon sequencing and denaturing gradient gel electrophoresis (DGGE) of naphthalene dioxygenase (ndo) genes were performed. Energy-dispersive X-ray spectroscopy (EDX) and atomic absorption spectroscopy (AAS) were performed to evaluate inorganic nutrients, and GC was performed to estimate aromatic compounds in the samples. The high frequency of Sphingomonadaceae in drip water samples indicates the presence of aromatic hydrocarbon-degrading bacteria. This finding was consistent with the detection of naphthalene and acenaphthene and the presence of ndo genes in drip-water-related samples. The aromatic compounds, aromatic hydrocarbon-degrading bacteria and 16S rDNA sequencing indicate that aromatic compounds may be one of the sources of energy and carbon to the system and the drip-water-associated bacterial community contains several potentially aromatic hydrocarbon-degrading bacteria. To the best of our knowledge, this is the first work to present compelling evidence for the presence of aromatic hydrocarbon-degrading bacteria in cave drip water.

Comparative analysis of microbiome between accurately identified 16S rDNA and quantified bacteria in simulated samples

2014 ◽  
Vol 63 (3) ◽  
pp. 433-440 ◽  
Author(s):  
Haiyin Wang ◽  
Pengcheng Du ◽  
Juan Li ◽  
Yuanyuan Zhang ◽  
Wen Zhang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
16S Rdna ◽  
Gold Standard ◽  
Clinical Utility ◽  
Bacterial Species ◽  
Relative Proportion ◽  
Rrna Gene ◽  
Low Concentrations ◽  
Rdna Sequencing ◽  
V3 Region

Although 16S rRNA gene (rDNA) sequencing is the gold standard for categorizing bacteria or characterizing microbial communities its clinical utility is limited by bias in metagenomic studies, in either the experiments or the data analyses. To evaluate the efficiency of current metagenomic methods, we sequenced seven simulated samples of ten bacterial species mixed at different concentrations. The V3 region of 16S rDNA was targeted and used to determine the distribution of bacterial species. The number of target sequences in individual simulated samples was in the range 1–1000 to provide a better reflection of natural microbial communities. However, for a given bacterial species present in the same proportion but at different concentrations, the observed percentage of 16S rDNAs was similar, except at very low concentrations that cannot be detected by real-time PCR. These results confirmed that the comparative microbiome in a sample characterized by 16S rDNA sequencing is sufficient to detect not only potential infectious pathogens, but also the relative proportion of 16S rDNA in the sample.

scholarly journals Effect of DNA Extraction Methods on the Apparent Structure of Yak Rumen Microbial Communities as Revealed by 16S rDNA Sequencing

2015 ◽  
Vol 64 (1) ◽  
pp. 29-36 ◽  
Author(s):  
YA-BING CHEN ◽  
DAO-LIANG LAN ◽  
CHENG TANG ◽  
XIAO-NONG YANG ◽  
JIAN LI
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Microbial Communities ◽  
16S Rdna ◽  
Dna Extraction ◽  
Extraction Methods ◽  
16S Rdna Sequencing ◽  
Bead Beating ◽  
Rdna Sequencing ◽  
Dna Extraction Methods

To more efficiently identify the microbial community of the yak rumen, the standardization of DNA extraction is key to ensure fidelity while studying environmental microbial communities. In this study, we systematically compared the efficiency of several extraction methods based on DNA yield, purity, and 16S rDNA sequencing to determine the optimal DNA extraction methods whose DNA products reflect complete bacterial communities. The results indicate that method 6 (hexadecyltrimethylammomium bromide-lysozyme-physical lysis by bead beating) is recommended for the DNA isolation of the rumen microbial community due to its high yield, operational taxonomic unit, bacterial diversity, and excellent cell-breaking capability. The results also indicate that the bead-beating step is necessary to effectively break down the cell walls of all of the microbes, especially Gram-positive bacteria. Another aim of this study was to preliminarily analyze the bacterial community via 16S rDNA sequencing. The microbial community spanned approximately 21 phyla, 35 classes, 75 families, and 112 genera. A comparative analysis showed some variations in the microbial community between yaks and cattle that may be attributed to diet and environmental differences. Interestingly, numerous uncultured or unclassified bacteria were found in yak rumen, suggesting that further research is required to determine the specific functional and ecological roles of these bacteria in yak rumen. In summary, the investigation of the optimal DNA extraction methods and the preliminary evaluation of the bacterial community composition of yak rumen support further identification of the specificity of the rumen microbial community in yak and the discovery of distinct gene resources.

scholarly journals Four different Phytophthora species that are able to infect Scots pine seedlings in laboratory conditions

2016 ◽  
Vol 58 (3) ◽  
pp. 123-130 ◽  
Author(s):  
Miłosz Tkaczyk ◽  
Katarzyna Sikora ◽  
Justyna A. Nowakowska ◽  
Ewa Aniśko ◽  
Tomasz Oszako ◽  
...  
Keyword(s):  
Scots Pine ◽  
Tissue Damage ◽  
Phytophthora Species ◽  
Control Group ◽  
Phytophthora Cactorum ◽  
Damping Off ◽  
Pine Seedlings ◽  
Forest Nurseries ◽  
Respective Species ◽  
Rule Out

Abstract To investigate susceptibility of young Scots pine seedlings to four Phytophthora species: Phytophthora cactorum, Phytophthora cambivora, Phytophthora plurivora and Phytophthora pini; seven-day-old seedlings of Scots pine (15 seedlings per experiment) were infected using agar plugs of the respective species. Control group also consisted of 15 seedlings and was inoculated with sterile agar plugs. Results unambiguously show that after 4.5 days, all seedlings show clear signs of infection and display severe symptoms of tissue damage and necrosis. Moreover, three and two seedlings in the P. cactorum and P. cambivora infected seedlings groups, respectively, collapsed. The length of largest necrosis measured 13.4±3.90 mm and was caused by P. cactorum. To rule out any putative contamination or infection by secondary pathogens, re-isolations of pathogens from infection sites were performed and were positive in 100% of plated pieces of infected seedlings. All re-isolations were, however, negative in the case of the control group. Detailed microscopic analyses of infected tissues of young seedlings confirmed the presence of numerous Phytophthora species inside and on the surface of infected seedlings. Therefore, our results suggest Phytophthora spp. and mainly P. cactorum and P. cambivora as aggressive pathogens of Scots pine seedlings and highlight a putative involvement of these species in the damping off of young Scots pine seedlings frequently observed in forest nurseries.

scholarly journals A REVIEW OF DAMPING-OFF OF DOUGLAS FIR SEEDLINGS IN BRITISH COLUMBIA

1954 ◽  
Vol 30 (4) ◽  
pp. 407-410 ◽  
Author(s):  
P. J. Salisbury
Keyword(s):  
British Columbia ◽  
Control Measures ◽  
Effective Control ◽  
Damping Off ◽  
Natural Control ◽  
Cover Soil ◽  
Low Degree ◽  
Nursery Practices ◽  
Forest Nurseries ◽  
And Control

Except in new nurseries, damping-off in British Columbia forest nurseries has remained below serious levels. Modification of nursery practices has served to reduce losses. The use of a suitable, sandy cover soil has been effective. Lowered fertility of the soil, though a problem in itself, appears to decrease incidence of damping-off. The acidity of the soil in coast nurseries may have afforded some natural control of the disease. From investigations on the control of damping-off, there appears to be promise in the use of peat as a planting medium for stratified seed, and, based on experiments with unstratified seed, in the application of fungicides to cover soil. In view of the present low degree of the disease, there would appear to be an opportunity for research directed to the biology and control of fungi known to be capable of causing sudden outbreaks, without the urgent need of finding immediately effective control measures.

Evaluation of soil solar heating for control of damping-off fungi in two forest nurseries in France

1997 ◽  
Vol 25 (2) ◽  
pp. 189-195 ◽  
Author(s):  
B. Le Bihan ◽  
P. Camporota ◽  
M. L. Soulas ◽  
M. I. Salerno ◽  
R. Perrin
Keyword(s):  
Solar Heating ◽  
Damping Off ◽  
Forest Nurseries

scholarly journals Ecology of seed-colonizing microbial communities: influence of soil and plant factors and implications for rhizosphere microbiology

2008 ◽  
Author(s):  
Dror Minz ◽  
Eric Nelson ◽  
Yitzhak Hadar
Keyword(s):  
Microbial Communities ◽  
Functional Significance ◽  
Disease Suppression ◽  
Pythium Species ◽  
Damping Off ◽  
Bacterial Consortia ◽  
Compost Amendment ◽  
Initial Work ◽  
Project Objectives ◽  
Carbon Competition

Original objectives: Our initial project objectives were to 1) Determine and compare the composition of seed-colonizing microbial communities on seeds, 2) Determine the dynamics of development of microbial communities on seeds, and 3) Determine and compare the composition of seed-colonizing microbial communities with the composition of those in the soil and rhizosphere of the plants.   Revisions to objectives: Our initial work on this project was hampered by the presence of native Pythium species in the soils we were using (in the US), preventing us from getting accurate assessments of spermosphere microbial communities. In our initial work, we tried to get around this problem by focusing on water potentials that might reduce damage from native Pythium species. This also prompted some initial investigation of the oomycete communities associated seedlings in this soil. However, for this work to proceed in a way that would allow us to examine seed-colonizing communities on healthy plants, we needed to either physically treat soils or amend soils with composts to suppress damage from Pythium. In the end, we followed the compost amendment line of investigation, which took us away from our initial objectives, but led to interesting work focusing on seed-associated microbial communities and their functional significance to seed-infecting pathogens. Work done in Israel was using suppressive compost amended potting mix throughout the study and did not have such problems. Our work focused on the following objectives: 1) to determine whether different plant species support a microbial induced suppression of Pythium damping-off, 2) to determine whether compost microbes that colonize seeds during early stages of seed germination can adequately explain levels of damping-off suppression observed, 3) to characterize cucumber seed-colonizing microbial communities that give rise to the disease suppressive properties, 4) assess carbon competition between seed-colonizing microbes and Pythium sporangia as a means of explaining Pythium damping-off suppression.  Background: Earlier work demonstrated that seed-colonizing microbes might explain Pythium suppression. Yet these seed-colonizing microbial communities have never been characterized and their functional significance to Pythium damping-off suppression is not known. Our work set out to confirm the disease suppressive properties of seed-colonizing microbes, to characterize communities, and begin to determine the mechanisms by which Pythium suppression occurs.  Major Conclusions: Compost-induced suppression of Pythium damping-off of cucumber and wheat can be explained by the bacterial consortia colonizing seeds within 8 h of sowing. Suppression on pea was highly variable. Fungi and archaea play no role in disease suppression. Potentially significant bacterial taxa are those with affinities to Firmicutes, Actinobacteria, and Bacteroidetes. Current sequencing efforts are trying to resolve these taxa. Seed colonizing bacteria suppress Pythium by carbon competition, allowing sporangium germination by preventing the development of germ tubes. Presence of Pythium had a strong effect on microbial community on the seed.

scholarly journals Deploying and in vitro gut model to assay the impact of a mannan-oligosaccharide prebiotic, Bio-MOS® on the Atlantic salmon (Salmo salar) gut microbiome

2020 ◽  
Author(s):  
R. Kazlauskaite ◽  
B. Cheaib ◽  
J. Humble ◽  
C. Heys ◽  
U. Ijaz ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Microbial Communities ◽  
Microbial Community Composition ◽  
Significant Shift ◽  
Gut Health ◽  
Mannan Oligosaccharide ◽  
Rdna Sequencing ◽  
The Impact

AbstractMannose-oligosaccharide (MOS) pre-biotics are widely deployed in animal agriculture as immunomodulators as well as to enhance growth and gut health. Their mode of action is thought to be mediated through their impact on host microbial communities and associated metabolism. Bio-MOS is a commercially available pre-biotic currently used in the agri-feed industry. To assay Bio-MOS for potential use as a pre-biotic growth promotor in salmonid aquaculture, we modified an established Atlantic salmon in vitro gut model, SalmoSim, to evaluate its impact on host microbial communities. In biological triplicate, microbial communities were stabilised in SalmoSim followed by twenty-day exposure to the pre-biotic and then an eight day ‘wash out’ period. Exposure the MOS resulted in a significant increase in formate (p=0.001), propionate (p=0.037) and isovalerate (p=0.024) levels, correlated with increased abundances of several principally anaerobic microbial genera (Fusobacteria, Agarivorans, Pseudoalteromonas, Myroides). 16S rDNA sequencing confirmed a significant shift in microbial community composition in response to supplementation. In conjunction with previous in vivo studies linking enhanced VFA production alongside MOS supplementation to host growth and performance, our data suggest that Bio-MOS may be of value in salmonid production. Furthermore, our data highlight the potential role of in vitro gut models to augment in vivo trials of microbiome modulators.

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