scholarly journals Detection of Pathogenic and Beneficial Microbes for Roselle Wilt Disease

2021 ◽  
Vol 12 ◽  
Author(s):  
Chih-Wei Wang ◽  
Yu-Hsiang Yu ◽  
Chun-Yao Wu ◽  
Ru-Ying Feng ◽  
Kshitij Tandon ◽  
...  
Keyword(s):  
Biocontrol Agent ◽  
Disease Status ◽  
Amplicon Sequencing ◽  
Wilt Disease ◽  
Operational Taxonomic Units ◽  
16S Rrna Amplicon Sequencing ◽  
Potential Biocontrol Agent ◽  
Main Target ◽  
Potential Pathogen ◽  
Bacterial Groups

Wilt disease of roselle (Hibiscus sabdariffa L.) is common in Taiwan; however, the causative agent remains unknown. The stems of wilted roselle are browned, slightly constricted, and covered by white aerial hyphae, suggesting that potential pathogens may originate from soil. To identify the potential pathogens, we conducted a rhizosphere microbiota survey in phenotypically healthy and diseased plants through fungal internal transcribed spacer (ITS) and bacterial 16S rRNA amplicon sequencing for uncovering the microbial compositions in the roselle rhizosphere. The fungal family Nectriaceae exhibited significantly higher abundance in diseased rhizospheres than in healthy rhizospheres, and this bacterial community was more specific to geography (i.e., plot-dependent) than to rhizosphere disease status. However, a few bacterial groups such as Bacilli were associated with the healthy rhizosphere. Fusarium species were the most dominant species of Nectriaceae in the survey and became the main target for potential pathogen isolation. We successfully isolated 119 strains from diseased plants in roselle fields. Koch’s postulates were used to evaluate the pathogenicity of these strains; our results indicated that Fusarium solani K1 (FsK1) can cause wilting and a rotted pith in roselles, which was consistent with observations in the fields. This is the first demonstration that F. solani can cause roselle wilt in Taiwan. Furthermore, these newly isolated strains are the most dominant operational taxonomic units detected in ITS amplicon sequencing in diseased rhizospheres, which serves as further evidence that F. solani is the main pathogen causing the roselle wilt disease. Administration of Bacillus velezensis SOI-3374, a strain isolated from a healthy roselle rhizosphere, caused considerable anti-FsK1 activity, and it can serve as a potential biocontrol agent against roselle wilt disease.

scholarly journals Newly Isolated Streptomyces sp. JBS5-6 as a Potential Biocontrol Agent to Control Banana Fusarium Wilt: Genome Sequencing and Secondary Metabolite Cluster Profiles

2020 ◽  
Vol 11 ◽  
Author(s):  
Tao Jing ◽  
Dengbo Zhou ◽  
Miaoyi Zhang ◽  
Tianyan Yun ◽  
Dengfeng Qi ◽  
...  
Keyword(s):  
Fusarium Wilt ◽  
Complete Genome ◽  
Biocontrol Agent ◽  
Fermentation Broth ◽  
Membrane Integrity ◽  
Gene Clusters ◽  
Wilt Disease ◽  
Gas Chromatography Mass Spectrometry ◽  
Fusarium Wilt Disease ◽  
Potential Biocontrol Agent

Banana is a key staple food and fruit in countries all over the world. However, the development of the global banana industry is seriously threatened by Fusarium wilt disease, which is caused by Fusarium oxysporum f. sp. cubense (Foc). In particular, Foc tropical race 4 (Foc TR4) could infect more than 80% of global banana and plantain crops. Until now, there were no commercial chemicals or resistant cultivars available to control the disease. Biological control using actinomycetes is considered a promising strategy. In this study, 88 actinomycetes were isolated from a banana orchard without symptoms of Fusarium wilt disease for more than 10 years. An actinobacterial strain labeled as JBS5-6 has exhibited strong antifungal activities against Foc TR4 and other selected 10 phytopathogenic fungi. Based on phenotypic and biochemical traits as well as complete genome analysis, strain JBS5-6 was assigned to Streptomyces violaceusniger. Extracts of the strain inhibited the mycelial growth and spore germination of Foc TR4 by destroying membrane integrity and the ultrastructure of cells. The complete genome of strain JBS5-6 was sequenced and revealed a number of key function gene clusters that contribute to the biosynthesis of active secondary metabolites. Sixteen chemical compounds were further identified by gas chromatography-mass spectrometry (GC-MS). 5-hydroxymethyl-2-furancarboxaldehyde was one of the dominant components in strain JBS5-6 extracts. Moreover, fermentation broth of strain JBS5-6 significantly reduced the disease index of banana seedlings by inhibiting the infection of Foc TR4 in a pot experiment. Hence, strain JBS5-6 is a potential biocontrol agent for the management of disease and the exploitation of biofertilizer.

scholarly journals The Effect of Coconut Oil Addition to Feed of Pigs on Rectal Microbial Diversity and Bacterial Abundance

Animals ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1764
Author(s):  
Michal Rolinec ◽  
Juraj Medo ◽  
Michal Gábor ◽  
Martina Miluchová ◽  
Daniel Bíro ◽  
...  
Keyword(s):  
Coconut Oil ◽  
Amplicon Sequencing ◽  
Normal Diet ◽  
Feeding Experiment ◽  
Bacterial Dna ◽  
Operational Taxonomic Units ◽  
Bacterial Groups ◽  
Sample Set ◽  
Positive Effect ◽  
Index Of Diversity

Coconut oil has a high content of lauric acid, which has selective antibacterial activity. This study aimed to explore the effect of coconut oil ingestion on the gastrointestinal microbiomes of pigs. A 14-day-long feeding experiment included 19 pigs in two groups (9 on a normal diet and 10 on a diet supplemented with coconut oil). At the start and end of the experiment, a rectal swab sample was taken from each pig in both groups, and total bacterial DNA was extracted. We used 16S rRNA high-throughput amplicon sequencing to evaluate the microbiome changes during the feeding experiment. A total of 446 operational taxonomic units (OTUs) were detected in the whole sample set. Shannon’s indices of bacterial diversity did not change significantly during the experiment. Changes in the bacterial community during the study period and in response to the coconut oil treatment were highly significant (p < 0.001). During the study, an increase in the abundance of Lactobacillus was detected in the group treated with coconut oil. An increase in Alloprevotella, Bifidobacteriales, and Lactobacillales and a decrease in Corynebacterium, Mitsuokella, Psychrobacter, and Pseudomonadales were attributed to the coconut oil treatment. Although the addition of coconut oil to pig feed did not affect Shannon’s index of diversity, it had a positive effect on the abundance of bacterial groups that are considered to be commensal and/or probiotic.

scholarly journals Experimental evidence pointing to rain as a reservoir of tomato phyllosphere microbiota

2021 ◽  
Author(s):  
Marco Enrique Mechan Llontop ◽  
Long Tian ◽  
Parul Sharma ◽  
Logan Heflin ◽  
Vivian Angelica Bernal Galeano ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Microbial Population ◽  
Amplicon Sequencing ◽  
Crop Productivity ◽  
Sterile Water ◽  
Tomato Plants ◽  
Operational Taxonomic Units ◽  
16S Rrna Amplicon Sequencing ◽  
Plant Microbiota

Plant microbiota play essential roles in plant health and crop productivity. Comparisons of community composition have suggested seeds, soil, and the atmosphere as reservoirs of phyllosphere microbiota. After finding that leaves of tomato (Solanum lycopersicum) plants exposed to rain carried a higher microbial population size than leaves of tomato plants not exposed to rain, we experimentally tested the hypothesis that rain is a so far neglected reservoir of phyllosphere microbiota. Rain microbiota were thus compared with phyllosphere microbiota of tomato plants either treated with concentrated rain microbiota, filter-sterilized rain, or sterile water. Based on 16S rRNA amplicon sequencing, one-hundred and four operational taxonomic units (OTUs) significantly increased in relative abundance after inoculation with concentrated rain microbiota but no OTU significantly increased after treatment with either sterile water or filter-sterilized rain. Some of the genera to which these 104 OTUs belonged were also found at higher relative abundance on tomatoes exposed to rain outdoors than on tomatoes grown protected from rain in a commercial greenhouse. Taken together, these results point to precipitation as a reservoir of phyllosphere microbiota and show the potential of controlled experiments to investigate the role of different reservoirs in the assembly of phyllosphere microbiota.

scholarly journals Korean Traditional Medicine (Jakyakgamcho-tang) Ameliorates Colitis by Regulating Gut Microbiota

Metabolites ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 226 ◽  
Author(s):  
Seung-Ho Seo ◽  
Tatsuya Unno ◽  
Seong-Eun Park ◽  
Eun-Ju Kim ◽  
Yu-Mi Lee ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Amplicon Sequencing ◽  
Control Group ◽  
Scaling Analysis ◽  
Aminosalicylic Acid ◽  
Operational Taxonomic Units ◽  
16S Rrna Amplicon Sequencing ◽  
Cytokine Levels ◽  
Korean Traditional Medicine ◽  
Gut Microbial Community

The objective of this study was to examine the anti-colitis activity of Jakyakgamcho-tang (JGT) in dextran sulfate sodium (DSS)-induced colitis and explore changes of the gut microbial community using 16S rRNA amplicon sequencing and metabolomics approaches. It was found that treatment with JGT or 5-aminosalicylic acid (5-ASA) alleviated the severity of colitis symptoms by suppressing inflammatory cytokine levels of IL-6, IL-12, and IFN-γ. The non-metric multidimensional scaling analysis of gut microbiome revealed that JGT groups were clearly separated from the DSS group, suggesting that JGT administration altered gut microbiota. The operational taxonomic units (OTUs) that were decreased by DSS but increased by JGT include Akkermansia and Allobaculum. On the other hand, OTUs that were increased by DSS but decreased by 5-ASA or JGT treatments include Bacteroidales S24-7, Ruminococcaceae, and Rikenellaceae, and the genera Bacteroides, Parabacteroides, Oscillospira, and Coprobacillus. After JGT administration, the metabolites, including most amino acids and lactic acid that were altered by colitis induction, became similar to those of the control group. This study demonstrates that JGT might have potential to effectively treat colitis by restoring dysbiosis of gut microbiota and host metabolites.

An investigation into the anaerobic spoilage microbiota of beef carcass and rump steak cuts using high- throughput sequencing

2021 ◽  
Author(s):  
Eden Esteves ◽  
Paul Whyte ◽  
John Mills ◽  
Gale Brightwell ◽  
Tanushree B Gupta ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Bioinformatics Analysis ◽  
Amplicon Sequencing ◽  
Alpha And Beta Diversity ◽  
Operational Taxonomic Units ◽  
16S Rrna Amplicon Sequencing ◽  
Meat Spoilage ◽  
Beef Carcasses ◽  
Spoilage Bacteria ◽  
Beef Carcass

Abstract The presence of anaerobic microflora on fresh beef carcass and rump steaks, which may contribute to meat spoilage, was explored in this study. A total of 120 carcass and 120 rump steak swabs were collected immediately after slaughtering and boning, respectively from five meat plants, anaerobically incubated and enriched d at 4°C for 3 weeks. This was followed by DNA extraction and 16S rRNA amplicon sequencing using the Illumina MiSeqTM, with subsequent bioinformatics analysis. The enriched microbiota of the samples was classified and grouped into 149 operational taxonomic units (OTUs). The microbiota recovered from both sample types consisted mainly of Carnobacterium, with an average relative abundance of 28.4% and 32.8% in beef carcasses and beef rump steaks, respectively. This was followed by Streptococcus, Serratia, Lactococcus, Enterococcus, Escherichia-Shigella, Raoultella and Aeromonas ranging from 1.5–20% and 0.1–29.8% in enriched carcasses and rump steak swabs, respectively. Trichococcus, Bacteroides, Dysgomonas, Providencia, Paraclostridium and Proteus were also present ranging from 0–0.8% on carcass and 0–1.8% on rump steak swabs, respectively. Alpha and Beta diversity measurements showed limited diversity between the two sample types, but some differences between samples from the beef plants investigated were evident. This study highlights the presence of potential spoilage bacteria, mainly anaerobic genera on and between carcass and rump steaks, as an indication of contamination on and between these samples.

scholarly journals Land Use Effects on Airborne Bacterial Communities Are Evident in Both Near-Surface and Higher-Altitude Air

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 85
Author(s):  
Allison M. Spring ◽  
Kenneth D. Domingue ◽  
Thomas V. Kerber ◽  
Margaret M. Mooney ◽  
Rebecca L. Hale ◽  
...  
Keyword(s):  
Land Use ◽  
Bacterial Communities ◽  
Amplicon Sequencing ◽  
Small Scale ◽  
Dispersal Patterns ◽  
Near Surface ◽  
Operational Taxonomic Units ◽  
16S Rrna Amplicon Sequencing ◽  
Surface Samples ◽  
Land Use Effects

Land use influences the composition of near-surface airborne bacterial communities, and bacteria can be transported through the atmosphere at global scales. The atmosphere mixes vertically, but rigorously assessing whether the effects of land use on atmospheric communities extends to higher altitudes requires examining communities from multiple altitudes collected at a stable location and timeframe. In this study, we collected near-surface (<2 m) and higher-altitude (150 m) air samples from three sites in an agricultural/developed location and a forested/undeveloped location. We used bacterial 16S rRNA amplicon sequencing to compare communities and predict functionality by altitude. Higher-altitude and near-surface communities did not differ in composition within each location. Communities collected above the undeveloped location were equally variable at both altitudes; higher-altitude samples from the developed location predominantly contained Firmicutes and were less variable than near-surface samples. We also compared airborne taxa to those present in soil and snow. Communities from higher-altitude samples above the developed location contained fewer overlapping taxa with soil and snow sources, and overlapping Operational Taxonomic Units (OTUs) among the three sources differed by location. Our results suggest that land use affects the composition of both near-surface and higher-altitude airborne bacterial communities and, therefore, may influence broad bacterial dispersal patterns. This small-scale pilot study provides a framework for simultaneously examining local and regional airborne microbial communities that can be applied to larger studies or studies using different types of samplers.

scholarly journals Experimental evidence pointing to rain as a reservoir of tomato phyllosphere microbiota

2021 ◽  
Author(s):  
Marco E Mechan Llontop ◽  
Long Tian ◽  
Parul Sharma ◽  
Logan Heflin ◽  
Vivian A Bernal-Galeano ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Microbial Population ◽  
Amplicon Sequencing ◽  
Crop Productivity ◽  
Sterile Water ◽  
Tomato Plants ◽  
Operational Taxonomic Units ◽  
16S Rrna Amplicon Sequencing ◽  
Plant Microbiota

Plant microbiota play essential roles in plant health and crop productivity. Comparisons of community composition have suggested seeds, soil, and the atmosphere as reservoirs of phyllosphere microbiota. After finding that leaves of tomato (Solanum lycopersicum) plants exposed to rain carried a higher microbial population size than leaves of tomato plants not exposed to rain, we experimentally tested the hypothesis that rain is a so far neglected reservoir of phyllosphere microbiota. Rain microbiota were thus compared with phyllosphere microbiota of tomato plants either treated with concentrated rain microbiota, filter-sterilized rain, or sterile water. Based on 16S rRNA amplicon sequencing, one-hundred and four operational taxonomic units (OTUs) significantly increased in relative abundance after inoculation with concentrated rain microbiota but no OTU significantly increased after treatment with either sterile water or filter-sterilized rain. Some of the genera to which these 104 OTUs belonged were also found at higher relative abundance on tomatoes exposed to rain outdoors than on tomatoes grown protected from rain in a commercial greenhouse. Taken together, these results point to precipitation as a reservoir of phyllosphere microbiota and show the potential of controlled experiments to investigate the role of different reservoirs in the assembly of phyllosphere microbiota.

Research advance on Esteya vermicola, a high potential biocontrol agent of pine wilt disease

2015 ◽  
Vol 14 (12) ◽  
Author(s):  
Wen Hui Chu ◽  
Qing Dou ◽  
Hong Long Chu ◽  
Hai Hua Wang ◽  
Chang Keun Sung ◽  
...  
Keyword(s):  
Biocontrol Agent ◽  
Pine Wilt Disease ◽  
Wilt Disease ◽  
High Potential ◽  
Pine Wilt ◽  
Potential Biocontrol Agent ◽  
Research Advance ◽  
Esteya Vermicola

What habitat does spiny snout mite occupy in Tasmania

2015 ◽  
Vol 68 ◽  
pp. 446-446
Author(s):  
D.J. Wilson ◽  
P.J. Gerard
Keyword(s):  
New Zealand ◽  
Sand Dune ◽  
Biocontrol Agent ◽  
Predatory Mites ◽  
Mite Species ◽  
Predatory Mite ◽  
Habitat Specificity ◽  
Nontarget Organisms ◽  
Flea Control ◽  
Potential Biocontrol Agent

Spiny snout mite (Neomolgus capillatus) is a potential biocontrol agent for clover flea (Sminthurus viridis) a white clover pest on dairy farms in warmer and wetter parts of New Zealand In the 1990s this mite was introduced from Brittany France into Tasmania for clover flea control Results during the release programme were highly promising and subsequent anecdotal farmer reports indicate widespread decreases in damage As N capillatus is a predatory mite and already known to attack nontarget organisms habitat specificity will determine whether it could be introduced into New Zealand without risk to native insects To assess this pastures on nine of the original Tasmanian release farms and adjacent nontarget habitats ranging from bush wetlands eucalypt stands to sand dune country were sampled in April 2014 Litter samples were collected heat extracted and mite species identified Neomolgus capillatus was found at effective densities in pastures that had good clover cover Where present it displaced Bdellodes spp mites that are ineffective against clover flea No N capillatus were found in the nontarget habitats all of which lacked clover and contained other predatory mites including Bdellodes spp Therefore the preference by N capillatus for lush pastures makes it an excellent prospect for introduction as a biocontrol agent into clover flea prone regions of New Zealand

scholarly journals Bacterial Diversity of Breast Milk in Healthy Spanish Women: Evolution from Birth to Five Years Postpartum

Nutrients ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 2414
Author(s):  
Laura Sanjulián ◽  
Alexandre Lamas ◽  
Rocío Barreiro ◽  
Alberto Cepeda ◽  
Cristina A. Fente ◽  
...  
Keyword(s):  
Breast Milk ◽  
16S Rrna ◽  
Human Milk ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Maternal Body Mass Index ◽  
16S Rrna Amplicon Sequencing ◽  
Spanish Women ◽  
Calcium Magnesium ◽  
Abundant Genus

The objective of this work was to characterize the microbiota of breast milk in healthy Spanish mothers and to investigate the effects of lactation time on its diversity. A total of ninety-nine human milk samples were collected from healthy Spanish women and were assessed by means of next-generation sequencing of 16S rRNA amplicons and by qPCR. Firmicutes was the most abundant phylum, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. Accordingly, Streptococcus was the most abundant genus. Lactation time showed a strong influence in milk microbiota, positively correlating with Actinobacteria and Bacteroidetes, while Firmicutes was relatively constant over lactation. 16S rRNA amplicon sequencing showed that the highest alpha-diversity was found in samples of prolonged lactation, along with wider differences between individuals. As for milk nutrients, calcium, magnesium, and selenium levels were potentially associated with Streptococcus and Staphylococcus abundance. Additionally, Proteobacteria was positively correlated with docosahexaenoic acid (DHA) levels in breast milk, and Staphylococcus with conjugated linoleic acid. Conversely, Streptococcus and trans-palmitoleic acid showed a negative association. Other factors such as maternal body mass index or diet also showed an influence on the structure of these microbial communities. Overall, human milk in Spanish mothers appeared to be a complex niche shaped by host factors and by its own nutrients, increasing in diversity over time.

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