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 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.

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 Comparative Analysis of Chicken Cecal Microbial Diversity and Taxonomic Composition in Response to Dietary Variation using 16S rRNA Amplicon Sequencing

2021 ◽  
Author(s):  
Zubia Rashid ◽  
Muhammad Zubair Yousaf ◽  
Syed Muddassar Hussain Gilani ◽  
Sitwat Zehra ◽  
Ashaq Ali ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Organic Acids ◽  
Microbial Diversity ◽  
Relative Abundance ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Feed Additives ◽  
Poultry Feed ◽  
16S Rrna Amplicon Sequencing

Abstract Antibiotic resistance poses a serious threat to human and animal health. As a consequence, their use in conventional poultry feed may be replaced by non-antibiotic additives (alternatives to antibiotics, ATAs). Phytogenic feed additives and organic acids have been gaining considerable attention that could abate the proliferation of pathogenic bacteria and strengthen gut function in broiler chickens. The aim of this study was to evaluate the effects of phytogenic feed additives and organic acids on cecal microbial diversity using 16S rRNA amplicon sequencing of the V3-V4 region. In this study, 240 chicks were divided into five treatments comprising: a controlled basal diet (CON), antibiotic group (AB), phytogenic feed additives (PHY), organic acids (ORG) and a combination of PHY + ORG (COM). A distinctive microbial community structure was observed amongst different treatments with an increased microbial diversity in AB, ORG and COM (p < 0.05). The synergistic effects of PHY and ORG increased the population of beneficial bacteria that belonged to the phyla: Firmicutes, Bacteroides and Proteobacteria in the cecum. The presence of the species Akkermansia muciniphila (involved in mucin degradation) and Bacillus safensis (a probiotic bacterium) were noticed in COM and PHY, respectively. Clustering analysis revealed a higher relative abundance of similar microbial community composition between AB and ORG groups. In conclusion, treatments with PHY and ORG modified the relative abundance and presence/absence of specific microbiota in the chicken cecum. Hence, cecal microbiota modulation through diet is a promising strategy to reduce cross-contamination of zoonotic poultry pathogens.

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 Features of morphogenesis, accumulation and redistribution of assimilate and nitrogen containing compounds in tomatoes under retardants treatment

2018 ◽  
Vol 8 (1) ◽  
pp. 356-362 ◽  
Author(s):  
V. G. Kuryata ◽  
O. O. Kravets
Keyword(s):  
Morphological Changes ◽  
Crop Productivity ◽  
Tomato Crop ◽  
Tomato Plants ◽  
Vegetative Organs ◽  
Palisade And Spongy Parenchyma ◽  
Source Sink ◽  
Sphere Formation ◽  
Nitrogen Containing Compounds

<p>We studied the influence of ethylene product Esphon® and triazole derivative Folicur® on the morphogenesis and productivity of tomatoes. The obtained results explained the significant role of morphological and mesostructural components of “source-sink” relation system of tomatoes in the formation of crop productivity. We established that the Folicur application resulted in more significant anatomical and morphological changes in the formation of leaf apparatus in comparison with the ethylene producer: the measurement of number, weight, area of leaf surface, and leaf index were higher in this variant of experiment. We also noted the appropriate changes in the mesostructure measurement of leaves: thickness of leave – main photosynthetic tissue of chlorenchyma, assimilatory cells size of palisade and spongy parenchyma. Analysis of depositing possibilities of plants vegetative organs at the fruitification stage indicates the importance of temporary postponement of nonstructural carbohydrates and nitrogen containing compounds in them followed by reutilization for carpogenesis needs. Application of Folicur resulted on the formation of a more powerful donor sphere and in the early fruit growth and formation stages are postponed more carbohydrates in vegetative organs of tomato plants compared to control. The content of sugars and starch in the roots, stems and leaves of plants under Folicur treatment was highest in all organs of the plant throughout the fruitification phase compared to control and variant with Esphon application. Our results also testify to the possibilities of nitrogen compounds remobilize from vegetative organs to carpogenesis needs. After Folicur treatment, the most intense decrease in the content of nitrogen containing compounds was observed during the transition from the fruit formation stage to green fruits stage in roots and stem of plant during the period of the most intense tomatoes growth. We concluded that a significant increase the yield of tomato crop was caused by the more powerful donor sphere formation and reutilization of assimilates and nitrogen containing compounds after Folicur application.</p>

scholarly journals A Simple Microbiome in the European Common Cuttlefish,Sepia officinalis

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Holly L. Lutz ◽  
S. Tabita Ramírez-Puebla ◽  
Lisa Abbo ◽  
Amber Durand ◽  
Cathleen Schlundt ◽  
...  
Keyword(s):  
Digestive Tract ◽  
Amplicon Sequencing ◽  
Sepia Officinalis ◽  
Content Type ◽  
16S Rrna Amplicon Sequencing ◽  
The Family ◽  
In Captivity ◽  
Small Clusters ◽  
Discrete Layer

ABSTRACTThe European common cuttlefish,Sepia officinalis, is used extensively in biological and biomedical research, yet its microbiome remains poorly characterized. We analyzed the microbiota of the digestive tract, gills, and skin in mariculture-raisedS. officinalisusing a combination of 16S rRNA amplicon sequencing, quantitative PCR (qPCR), and fluorescence spectral imaging. Sequencing revealed a highly simplified microbiota consisting largely of two single bacterial amplicon sequence variants (ASVs) ofVibrionaceaeandPiscirickettsiaceae. The esophagus was dominated by a single ASV of the genusVibrio. Imaging revealed bacteria in the familyVibrionaceaedistributed in a discrete layer that lines the esophagus. ThisVibriowas also the primary ASV found in the microbiota of the stomach, cecum, and intestine, but occurred at lower abundance, as determined by qPCR, and was found only scattered in the lumen rather than in a discrete layer via imaging analysis. Treatment of animals with the commonly used antibiotic enrofloxacin led to a nearly 80% reduction of the dominantVibrioASV in the esophagus but did not significantly alter the relative abundance of bacteria overall between treated versus control animals. Data from the gills were dominated by a single ASV in the familyPiscirickettsiaceae, which imaging visualized as small clusters of cells. We conclude that bacteria belonging to theGammaproteobacteriaare the major symbionts of the cuttlefishSepia officinaliscultured from eggs in captivity and that the esophagus and gills are major colonization sites.IMPORTANCEMicrobes can play critical roles in the physiology of their animal hosts, as evidenced in cephalopods by the role ofVibrio(Aliivibrio)fischeriin the light organ of the bobtail squid and the role ofAlpha- andGammaproteobacteriain the reproductive system and egg defense in a variety of cephalopods. We sampled the cuttlefish microbiome throughout the digestive tract, gills, and skin and found dense colonization of an unexpected site, the esophagus, by a microbe of the genusVibrio, as well as colonization of gills byPiscirickettsiaceae. This finding expands the range of organisms and body sites known to be associated withVibrioand is of potential significance for understanding host-symbiont associations, as well as for understanding and maintaining the health of cephalopods in mariculture.

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 A simple microbiome in the European common cuttlefish, Sepia officinalis

2018 ◽  
Author(s):  
Holly L. Lutz ◽  
S. Tabita Ramírez-Puebla ◽  
Lisa Abbo ◽  
Amber Durand ◽  
Cathleen Schlundt ◽  
...  
Keyword(s):  
Digestive Tract ◽  
Amplicon Sequencing ◽  
Sepia Officinalis ◽  
16S Rrna Amplicon Sequencing ◽  
The Family ◽  
In Captivity ◽  
Aliivibrio Fischeri ◽  
Small Clusters ◽  
Discrete Layer

ABSTRACTThe European common cuttlefish, Sepia officinalis, is used extensively in biological and biomedical research yet its microbiome remains poorly characterized. We analyzed the microbiota of the digestive tract, gills, and skin in mariculture-raised S. officinalis using a combination of 16S rRNA amplicon sequencing, qPCR and fluorescence spectral imaging. Sequencing revealed a highly simplified microbiota consisting largely of two single bacterial amplicon sequence variants (ASVs) of Vibrionaceae and Piscirickettsiaceae. The esophagus was dominated by a single ASV of the genus Vibrio. Imaging revealed bacteria in the family Vibrionaceae distributed in a discrete layer that lines the esophagus. This Vibrio was also the primary ASV found in the microbiota of the stomach, cecum, and intestine, but occurred at lower abundance as determined by qPCR and was found only scattered in the lumen rather than in a discrete layer via imaging analysis. Treatment of animals with the commonly-used antibiotic enrofloxacin led to a nearly 80% reduction of the dominant Vibrio ASV in the esophagus but did not significantly alter the relative abundance of bacteria overall between treated versus control animals. Data from the gills was dominated by a single ASV in the family Piscirickettsiaceae, which imaging visualized as small clusters of cells. We conclude that bacteria belonging to the Gammaproteobacteria are the major symbionts of the cuttlefish Sepia officinalis cultured from eggs in captivity, and that the esophagus and gills are major colonization sites.IMPORTANCEMicrobes can play critical roles in the physiology of their animal hosts, as evidenced in cephalopods by the role of Vibrio (Aliivibrio) fischeri in the light organ of the bobtail squid and the role of Alpha- and Gammaproteobacteria in the reproductive system and egg defense in a variety of cephalopods. We sampled the cuttlefish microbiome throughout the digestive tract, gills, and skin and found dense colonization of an unexpected site, the esophagus, by a microbe of the genus Vibrio, as well as colonization of gills by Piscirickettsiaceae. This finding expands the range of organisms and body sites known to be associated with Vibrio and is of potential significance for understanding host-symbiont associations as well as for understanding and maintaining the health of cephalopods in mariculture.

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