scholarly journals The Resistance of Peanut to Soil-Borne Pathogens Improved by Rhizosphere Probiotics Under Calcium Treatment

2021 ◽  
Author(s):  
Wei Zhang ◽  
Bo-wen Zhang ◽  
Lin Li ◽  
Tu-yong Yi ◽  
Yan-yun Hong
Keyword(s):  
Serratia Marcescens ◽  
Plant Disease Resistance ◽  
Sclerotium Rolfsii ◽  
Amplicon Sequencing ◽  
Seedling Stage ◽  
Growth Stages ◽  
Calcium Treatment ◽  
Soil Borne Pathogens ◽  
16S Amplicon Sequencing ◽  
And Control

Abstract Background: Peanut (Arachis hypogaea L.) is an important oil and economic crop. Calcium can regulate plant autoimmunity, respond to biotic and abiotic stresses, and improve plant resistance to pathogens. The enrichment of beneficial microorganisms in the rhizosphere is related to plant disease resistance and soil development. The purpose was to analyze the differences of peanut rhizosphere microbial community structure between calcium treatment and control during two growth stages, and the reason that calcium application could improve peanut’s resistance to soil-borne pathogens.. Results: The 16S amplicon sequencing of rhizosphere microbiome showed that calcium application significantly enriched Serratia marcescens and other three dominant strains at the seedling stage. At the pod filling stage, ten dominant stains such as Sphingomonas changbaiensis and Novosphingobium panipatense were enriched by calcium. Serratia marcescens aseptic fermentation filtrate was mixed with PDA medium and inoculated with soil-borne pathogens, which could inhibit the growth of Fusarium solani and Aspergillus flavus at the seedling stage. The fermentation filtrate of Novosphingobium panipatense was mixed with PDA medium and inoculated with main pathogens, which could inhibit the growth of Sclerotium rolfsii and Leptosphaerulina arachidicola.Conclusions: Calcium application enhanced the ability of peanuts to resist pathogens by enriching specific dominant bacteria.

scholarly journals The resistance of peanut to soil-borne pathogens improved by rhizosphere probiotics under calcium treatment

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Wei Zhang ◽  
Bo-wen Zhang ◽  
Jie-fu Deng ◽  
Lin Li ◽  
Tu-yong Yi ◽  
...  
Keyword(s):  
Serratia Marcescens ◽  
Plant Disease Resistance ◽  
Sclerotium Rolfsii ◽  
Amplicon Sequencing ◽  
Seedling Stage ◽  
Growth Stages ◽  
Calcium Treatment ◽  
Filling Stage ◽  
Soil Borne Pathogens ◽  
16S Rdna Amplicon Sequencing

Abstract Background Peanut (Arachis hypogaea L.) is an important oil and economic crop. Calcium modulates plants in response to abiotic stresses and improves plant resistance to pathogens. Enrichment of beneficial microorganisms in the rhizosphere is associated with plant disease resistance and soil development. The purpose of this study was to analyze the differences in peanut rhizosphere microbial community structure between the calcium treatment and the control during two growth stages and to explain why calcium application could improve the resistance of peanuts to soil-borne pathogens. Results The 16S rDNA amplicon sequencing of rhizosphere microbiome showed that calcium application significantly enriched Serratia marcescens and other three dominant strains at the seedling stage. At the pod filling stage, ten dominant stains such as Sphingomonas changbaiensis and Novosphingobium panipatense were enriched by calcium. Serratia marcescens aseptic fermentation filtrate was mixed with PDA medium and inoculated with the main soil-borne pathogens in the seedling stage, which could inhibit the growth of Fusarium solani and Aspergillus flavus. The aseptic fermentation filtrate of Novosphingobium panipatense was mixed with PDA medium and inoculated with the main soil-borne pathogens in the pod filling stage, which could inhibit the growth of Sclerotium rolfsii and Leptosphaerulina arachidicola. Conclusions Calcium application increases the resistance of peanuts to soil-borne pathogens by enriching them with specific dominant bacteria.

scholarly journals SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tzipi Braun ◽  
Shiraz Halevi ◽  
Rotem Hadar ◽  
Gilate Efroni ◽  
Efrat Glick Saar ◽  
...  
Keyword(s):  
Clinical Microbiology ◽  
Amplicon Sequencing ◽  
Viral Disease ◽  
Nasopharyngeal Swab ◽  
Microbial Composition ◽  
16S Amplicon Sequencing ◽  
The World ◽  
Health And Disease ◽  
Longitudinal Sampling ◽  
Potential Interactions

AbstractThe coronavirus disease 2019 (COVID-19) has rapidly spread around the world, impacting the lives of many individuals. Growing evidence suggests that the nasopharyngeal and respiratory tract microbiome are influenced by various health and disease conditions, including the presence and the severity of different viral disease. To evaluate the potential interactions between Severe Acute Respiratory Syndrome Corona 2 (SARS-CoV-2) and the nasopharyngeal microbiome. Microbial composition of nasopharyngeal swab samples submitted to the clinical microbiology lab for suspected SARS-CoV-2 infections was assessed using 16S amplicon sequencing. The study included a total of 55 nasopharyngeal samples from 33 subjects, with longitudinal sampling available for 12 out of the 33 subjects. 21 of the 33 subjects had at least one positive COVID-19 PCR results as determined by the clinical microbiology lab. Inter-personal variation was the strongest factor explaining > 75% of the microbial variation, irrespective of the SARS-CoV-2 status. No significant effect of SARS-CoV-2 on the nasopharyngeal microbial community was observed using multiple analysis methods. These results indicate that unlike some other viruses, for which an effect on the microbial composition was noted, SARS-CoV-2 does not have a strong effect on the nasopharynx microbial habitants.

scholarly journals The dysbiosis of ovine foot microbiome during the development and treatment of contagious ovine digital dermatitis

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
J. S. Duncan ◽  
J. W. Angell ◽  
P. Richards ◽  
L. Lenzi ◽  
G. J. Staton ◽  
...  
Keyword(s):  
Antibiotic Treatment ◽  
Amplicon Sequencing ◽  
Strong Tendency ◽  
Rrna Gene ◽  
Digital Dermatitis ◽  
Healthy State ◽  
Foot Disease ◽  
End Stage ◽  
And Control ◽  
Interdigital Dermatitis

Abstract Background Contagious Ovine Digital Dermatitis (CODD) is an emerging and common infectious foot disease of sheep which causes severe welfare and economic problems for the sheep industry. The aetiology of the disease is not fully understood and control of the disease is problematic. The aim of this study was to investigate the polybacterial aetiopathogenesis of CODD and the effects of antibiotic treatment, in a longitudinal study of an experimentally induced disease outbreak using a 16S rRNA gene amplicon sequencing approach. Results CODD was induced in 15/30 experimental sheep. During the development of CODD three distinct phenotypic lesion stages were observed. These were an initial interdigital dermatitis (ID) lesion, followed by a footrot (FR) lesion, then finally a CODD lesion. Distinct microbiota were observed for each lesion in terms of microbial diversity, clustering and composition. Porphyromonadaceae, Family XI, Veillonellaceae and Fusobacteriaceae were significantly associated with the diseased feet. Veillonellaceae and Fusobacteriaceae were most associated with the earlier stages of ID and footrot rather than CODD. Following antibiotic treatment of the sheep, the foot microbiota showed a strong tendency to return to the composition of the healthy state. The microbiota composition of CODD lesions collected by swab and biopsy methods were different. In particular, the Spirochaetaceae family were more abundant in samples collected by the biopsy method, suggesting that these bacteria are present in deeper tissues of the diseased foot. Conclusion In this study, CODD presented as part of a spectrum of poly-bacterial foot disease strongly associated with bacterial families Porphyromonadaceae, Family XI (a family in Clostridiales also known as Clostridium cluster XI), Veillonellaceae and Fusobacteriaceae which are predominately Gram-negative anaerobes. Following antibiotic treatment, the microbiome showed a strong tendency to return to the composition of the healthy state. The composition of the healthy foot microbiome does not influence susceptibility to CODD. Based on the data presented here and that CODD appears to be the severest end stage of sheep infectious foot disease lesions, better control of the initial ID and FR lesions would enable better control of CODD and enable better animal welfare.

Evaluation of weed control in acetyl coA carboxylase-resistant rice with mixtures of quizalofop and auxinic herbicides

2019 ◽  
Vol 34 (4) ◽  
pp. 498-505
Author(s):  
Tameka L. Sanders ◽  
Jason A. Bond ◽  
Benjamin H. Lawrence ◽  
Bobby R. Golden ◽  
Thomas W. Allen ◽  
...  
Keyword(s):  
Weed Control ◽  
Rice Yield ◽  
Field Studies ◽  
Growth Stages ◽  
Acetyl Coa Carboxylase ◽  
Acetyl Coa ◽  
Herbicide Treatments ◽  
Herbicide Mixture ◽  
Sequential Treatments ◽  
And Control

AbstractRice with enhanced tolerance to herbicides that inhibit acetyl coA carboxylase (ACCase) allows POST application of quizalofop, an ACCase-inhibiting herbicide. Two concurrent field studies were conducted in 2017 and 2018 near Stoneville, MS, to evaluate control of grass (Grass Study) and broadleaf (Broadleaf Study) weeds with sequential applications of quizalofop alone and in mixtures with auxinic herbicides applied in the first or second application. Sequential treatments of quizalofop were applied at 119 g ai ha−1 alone and in mixtures with labeled rates of auxinic herbicides to rice at the two- to three-leaf (EPOST) or four-leaf to one-tiller (LPOST) growth stages. In the Grass Study, no differences in rice injury or control of volunteer rice (‘CL151’ and ‘Rex’) were detected 14 and 28 d after last application (DA-LPOST). Barnyardgrass control at 14 and 28 DA-LPOST with quizalofop applied alone or with auxinic herbicides EPOST was ≥93% for all auxinic herbicide treatments except penoxsulam plus triclopyr. Barnyardgrass control was ≥96% with quizalofop applied alone and with auxinic herbicides LPOST. In the Broadleaf Study, quizalofop plus florpyrauxifen-benzyl controlled more Palmer amaranth 14 DA-LPOST than other mixtures with auxinic herbicides, and control with this treatment was greater EPOST compared with LPOST. Hemp sesbania control 14 DA-LPOST was ≤90% with quizalofop plus quinclorac LPOST, orthosulfamuron plus quinclorac LPOST, and triclopyr EPOST or LPOST. All mixtures except quinclorac and orthosulfamuron plus quinclorac LPOST controlled ivyleaf morningglory ≥91% 14 DA-LPOST. Florpyrauxifen-benzyl or triclopyr were required for volunteer soybean control >63% 14 DA-LPOST. To optimize barnyardgrass control and rice yield, penoxsulam plus triclopyr and orthosulfamuron plus quinclorac should not be mixed with quizalofop. Quizalofop mixtures with auxinic herbicides are safe and effective for controlling barnyardgrass, volunteer rice, and broadleaf weeds in ACCase-resistant rice, and the choice of herbicide mixture could be adjusted based on weed spectrum in the treated field.

scholarly journals Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gongchao Jing ◽  
Yufeng Zhang ◽  
Wenzhi Cui ◽  
Lu Liu ◽  
Jian Xu ◽  
...  
Keyword(s):  
16S Rrna ◽  
Large Scale ◽  
Low Cost ◽  
Human Microbiome ◽  
Amplicon Sequencing ◽  
Training Sample ◽  
Rrna Gene ◽  
16S Amplicon Sequencing ◽  
Cross Platform ◽  
Functional Profiles

Abstract Background Due to their much lower costs in experiment and computation than metagenomic whole-genome sequencing (WGS), 16S rRNA gene amplicons have been widely used for predicting the functional profiles of microbiome, via software tools such as PICRUSt 2. However, due to the potential PCR bias and gene profile variation among phylogenetically related genomes, functional profiles predicted from 16S amplicons may deviate from WGS-derived ones, resulting in misleading results. Results Here we present Meta-Apo, which greatly reduces or even eliminates such deviation, thus deduces much more consistent diversity patterns between the two approaches. Tests of Meta-Apo on > 5000 16S-rRNA amplicon human microbiome samples from 4 body sites showed the deviation between the two strategies is significantly reduced by using only 15 WGS-amplicon training sample pairs. Moreover, Meta-Apo enables cross-platform functional comparison between WGS and amplicon samples, thus greatly improve 16S-based microbiome diagnosis, e.g. accuracy of gingivitis diagnosis via 16S-derived functional profiles was elevated from 65 to 95% by WGS-based classification. Therefore, with the low cost of 16S-amplicon sequencing, Meta-Apo can produce a reliable, high-resolution view of microbiome function equivalent to that offered by shotgun WGS. Conclusions This suggests that large-scale, function-oriented microbiome sequencing projects can probably benefit from the lower cost of 16S-amplicon strategy, without sacrificing the precision in functional reconstruction that otherwise requires WGS. An optimized C++ implementation of Meta-Apo is available on GitHub (https://github.com/qibebt-bioinfo/meta-apo) under a GNU GPL license. It takes the functional profiles of a few paired WGS:16S-amplicon samples as training, and outputs the calibrated functional profiles for the much larger number of 16S-amplicon samples.

scholarly journals Larval Diet Abundance Influences Size and Composition of the Midgut Microbiota of Aedes aegypti Mosquitoes

2021 ◽  
Vol 12 ◽  
Author(s):  
Hannah J. MacLeod ◽  
George Dimopoulos ◽  
Sarah M. Short
Keyword(s):  
Aedes Aegypti ◽  
Bacterial Load ◽  
Amplicon Sequencing ◽  
Larval Diet ◽  
Microbiota Composition ◽  
Vector Species ◽  
Larval Food ◽  
Disease Vector ◽  
16S Amplicon Sequencing ◽  
The Impact

The midgut microbiota of the yellow fever mosquito Aedes aegypti impacts pathogen susceptibility and transmission by this important vector species. However, factors influencing the composition and size of the microbiome in mosquitoes are poorly understood. We investigated the impact of larval diet abundance during development on the composition and size of the larval and adult microbiota by rearing Aedes aegypti under four larval food regimens, ranging from nutrient deprivation to nutrient excess. We assessed the persistent impacts of larval diet availability on the microbiota of the larval breeding water, larval mosquitoes, and adult mosquitoes under sugar and blood fed conditions using qPCR and high-throughput 16S amplicon sequencing to determine bacterial load and microbiota composition. Bacterial loads in breeding water increased with increasing larval diet. Larvae reared with the lowest diet abundance had significantly fewer bacteria than larvae from two higher diet treatments, but not from the highest diet abundance. Adults from the lowest diet abundance treatment had significantly fewer bacteria in their midguts compared to all higher diet abundance treatments. Larval diet amount also had a significant impact on microbiota composition, primarily within larval breeding water and larvae. Increasing diet correlated with increased relative levels of Enterobacteriaceae and Flavobacteriaceae and decreased relative levels of Sphingomonadaceae. Multiple individual OTUs were significantly impacted by diet including one mapping to the genus Cedecea, which increased with higher diet amounts. This was consistent across all sample types, including sugar fed and blood fed adults. Taken together, these data suggest that availability of diet during development can cause lasting shifts in the size and composition of the microbiota in the disease vector Aedes aegypti.

scholarly journals Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0241529
Author(s):  
Anita Silver ◽  
Sean Perez ◽  
Melanie Gee ◽  
Bethany Xu ◽  
Shreeya Garg ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Ground Beetle ◽  
Amplicon Sequencing ◽  
Carabid Beetles ◽  
Secretory Cells ◽  
Pygidial Gland ◽  
Defensive Compounds ◽  
Highly Active ◽  
16S Amplicon Sequencing ◽  
Host Diet

Host-associated microbiomes can play important roles in the ecology and evolution of their insect hosts, but bacterial diversity in many insect groups remains poorly understood. Here we examine the relationship between host environment, host traits, and microbial diversity in three species in the ground beetle family (Coleoptera: Carabidae), a group of roughly 40,000 species that synthesize a wide diversity of defensive compounds. This study used 16S amplicon sequencing to profile three species that are phylogenetically distantly related, trophically distinct, and whose defensive chemical secretions differ: Anisodactylus similis LeConte, 1851, Pterostichus serripes (LeConte, 1875), and Brachinus elongatulus Chaudoir, 1876. Wild-caught beetles were compared to individuals maintained in the lab for two weeks on carnivorous, herbivorous, or starvation diets (n = 3 beetles for each species-diet combination). Metagenomic samples from two highly active tissue types—guts, and pygidial gland secretory cells (which produce defensive compounds)—were processed and sequenced separately from those of the remaining body. Bacterial composition and diversity of these ground beetles were largely resilient to controlled changes to host diet. Different tissues within the same beetle harbor unique microbial communities, and secretory cells in particular were remarkably similar across species. We also found that these three carabid species have patterns of microbial diversity similar to those previously found in carabid beetles. These results provide a baseline for future studies of the role of microbes in the diversification of carabids.

Rhopalosiphum rufiabdominalis (rice root aphid).

2021 ◽  
Author(s):  
Angela Whittaker
Keyword(s):  
Upland Rice ◽  
Early Growth ◽  
Seedling Stage ◽  
Rice Root ◽  
Growth Stages ◽  
Light Damage ◽  
Irrigated Rice ◽  
The World ◽  
Heavy Damage ◽  
Economic Pest

Abstract R. rufiabdominalis is an economic pest of upland rice, particularly in Japan, but is not a pest of irrigated rice anywhere in the world (Grist and Lever, 1969). Injury to upland rice can be severe in Japan, with losses of up to 50-70% (Yano et al., 1983). Occurrence was related to the cultivars of upland rice in China, where aphids caused light damage at the seedling stage and heavy damage at the tillering stage (Ding, 1985). Generally, aphids cause more serious damage during the early growth stages (Yano et al., 1983).

Changes in the gut microbiota of morbidly obese patients after laparoscopic sleeve gastrectomy

2021 ◽  
Author(s):  
Alev Kural ◽  
Imran Khan ◽  
Hakan Seyit ◽  
Tuba R Caglar ◽  
Pınar Toklu ◽  
...  
Keyword(s):  
Sleeve Gastrectomy ◽  
Gut Microbiota ◽  
Laparoscopic Sleeve Gastrectomy ◽  
Amplicon Sequencing ◽  
Morbidly Obese ◽  
Microbiota Composition ◽  
16S Amplicon Sequencing ◽  
Before And After ◽  
Stool Samples ◽  
Gut Microbiota Composition

Aims: Permanent treatment of morbid obesity with medication or diet is nearly impossible. Laparoscopic sleeve gastrectomy (LSG) is becoming a widely accepted treatment option. This study profiled and compared gut microbiota composition before and after LSG. Methods & results: A total of 54 stool samples were collected from 27 morbidly obese individuals before and after LSG. The gut microbiota was profiled with 16S amplicon sequencing. After LSG, patients demonstrated a significant decrease (p < 0.001) in BMI and an increase in bacterial diversity. An increased Firmicutes/Bacteroidetes ratio was also noticed after LSG. The families Prevotellaceae and Veillonellaceae predominated in preoperative samples but were markedly lowered after LSG. A marked increase in Akkermansia, Alistipes, Streptococcus, Ruminococcus and Parabacteroides was observed after LSG. Conclusion: In addition to lowering BMI, LSG remodeled gut microbiota composition.

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