scholarly journals Mango Endophyte and Epiphyte Microbiome Composition during Fruit Development and Post-Harvest Stages

Horticulturae ◽  
2021 ◽  
Vol 7 (11) ◽  
pp. 495
Author(s):  
Malick Bill ◽  
Lizyben Chidamba ◽  
Jarishma Keriuscia Gokul ◽  
Lise Korsten
Keyword(s):  
Fruit Development ◽  
Management Strategies ◽  
Development Stage ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
Bacterial Phyla ◽  
Post Harvest ◽  
Bacterial Microbiota ◽  
Target Effect ◽  
Generation Sequencing

The influence of the development stage and post-harvest handling on the microbial composition of mango fruit plays a central role in fruit health. Hence, the composition of fungal and bacterial microbiota on the anthoplane, fructoplane, stems and stem-end pulp of mango during fruit development and post-harvest handling were determined using next-generation sequencing of the internal transcribed spacer and 16S rRNA regions. At full bloom, the inflorescence had the richest fungal and bacterial communities. The young developing fruit exhibited lower fungal richness and diversities in comparison to the intermediate and fully developed fruit stages on the fructoplane. At the post-harvest stage, lower fungal and bacterial diversities were observed following prochloraz treatment both on the fructoplane and stem-end pulp. Ascomycota (52.8%) and Basidiomycota (43.2%) were the most dominant fungal phyla, while Penicillium, Botryosphaeria, Alternaria and Mucor were detected as the known post-harvest decay-causing fungal genera. The Cyanobacteria (35.6%), Firmicutes (26.1%) and Proteobacteria (23.1%) were the most dominant bacterial phyla. Changes in the presence of Bacillus subtilis following post-harvest interventions such as prochloraz suggested a non-target effect of the fungicide. The present study, therefore, provides the primary baseline data on mango fungal and bacterial diversity and composition, which can be foundational in the development of effective disease (stem-end rot) management strategies.

scholarly journals Regional biogeography of microbiota composition in the Chagas disease vector Rhodnius pallescens

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Troy J. Kieran ◽  
Kaylee M. H. Arnold ◽  
Jesse C. Thomas ◽  
Christina P. Varian ◽  
Azael Saldaña ◽  
...  
Keyword(s):  
Microbial Ecology ◽  
Chagas Disease ◽  
Management Strategies ◽  
Geographical Location ◽  
Protozoan Parasite ◽  
Illumina Miseq ◽  
Whole Body ◽  
Microbial Composition ◽  
Bacterial Phyla ◽  
Rhodnius Pallescens

Abstract Background Triatomine bugs are vectors of the protozoan parasite Trypanosoma cruzi, which causes Chagas disease. Rhodnius pallescens is a major vector of Chagas disease in Panama. Understanding the microbial ecology of disease vectors is important in the development of vector management strategies that target vector survival and fitness. In this study we examined the whole-body microbial composition of R. pallescens from three locations in Panama. Methods We collected 89 R. pallescens specimens using Noireau traps in Attalea butyracea palms. We then extracted total DNA from whole-bodies of specimens and amplified bacterial microbiota using 16S rRNA metabarcoding PCR. The 16S libraries were sequenced on an Illumina MiSeq and analyzed using QIIME2 software. Results We found Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes to be the most abundant bacterial phyla across all samples. Geographical location showed the largest difference in microbial composition with northern Veraguas Province having the most diversity and Panama Oeste Province localities being most similar to each other. Wolbachia was detected in high abundance (48–72%) at Panama Oeste area localities with a complete absence of detection in Veraguas Province. No significant differences in microbial composition were detected between triatomine age class, primary blood meal source, or T. cruzi infection status. Conclusions We found biogeographical regions differ in microbial composition among R. pallescens populations in Panama. While overall the microbiota has bacterial taxa consistent with previous studies in triatomine microbial ecology, locality differences are an important observation for future studies. Geographical heterogeneity in microbiomes of vectors is an important consideration for future developments that leverage microbiomes for disease control.

scholarly journals Characterization of the bacterial microbiota composition and evolution at different intestinal tract in wild pigs (Sus scrofa ussuricus)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9124
Author(s):  
Guangli Yang ◽  
Chuanxin Shi ◽  
Shuhong Zhang ◽  
Yan Liu ◽  
Zhiqiang Li ◽  
...  
Keyword(s):  
Intestinal Microbiome ◽  
Microbial Composition ◽  
Intestinal Microbes ◽  
Domestic Pigs ◽  
Microbiome Composition ◽  
Wild Pigs ◽  
Evolutionary Forces ◽  
Bacterial Microbiota ◽  
And Function ◽  
Functional Analyses

Commensal microorganisms are essential to the normal development and function of many aspects of animal biology, including digestion, nutrient absorption, immunological development, behaviors, and evolution. The specific microbial composition and evolution of the intestinal tracts of wild pigs remain poorly characterized. This study therefore sought to assess the composition, distribution, and evolution of the intestinal microbiome of wild pigs. For these analyses, 16S rRNA V3-V4 regions from five gut sections prepared from each of three wild sows were sequenced to detect the microbiome composition. These analyses revealed the presence of 6,513 operational taxonomic units (OTUs) mostly distributed across 17 phyla and 163 genera in these samples, with Firmicutes and Actinobacteria being the most prevalent phyla of microbes present in cecum and jejunum samples, respectively. Moreover, the abundance of Actinobacteria in wild pigs was higher than that in domestic pigs. At the genus level the Bifidobacterium and Allobaculum species of microbes were most abundant in all tested gut sections, with higher relative abundance in wild pigs relative to domestic pigs, indicating that in the process of pig evolution, the intestinal microbes also evolved, and changes in the intestinal microbial diversity could have been one of the evolutionary forces of pigs. Intestinal microbial functional analyses also revealed the microbes present in the small intestine (duodenum, jejunum, and ileum) and large intestine (cecum and colon) of wild pigs to engage distinct metabolic spatial structures and pathways relative to one another. Overall, these results offer unique insights that would help to advance the current understanding of how the intestinal microbes interact with the host and affect the evolution of pigs.

Plant-Microbiome Interactions for Bacterial Wilt Suppression in Modern Tobacco Production

2020 ◽  
Author(s):  
Raymond O. García-Rodríguez ◽  
Lindsey D. Thiessen
Keyword(s):  
Management Strategies ◽  
Soil Health ◽  
Disease Suppression ◽  
Current Management ◽  
Core Microbiome ◽  
Microbiome Composition ◽  
Sequencing Technologies ◽  
Bacterial Microbiota ◽  
Culture Independent ◽  
Functional Capacities

The soil-borne bacterium Ralstonia solanacearum continues to represent a major threat to flue-cured tobacco (Nicotiana tabacum) production in the southeastern United States and other major producing regions throughout the world. Beneficial microorganisms naturally found in the soil represent an alternative solution for R. solanacearum’s suppression that may reduce soil health impacts of current management strategies. Biological controls and microbiota manipulation together represent a unique opportunity to reduce disease caused by R. solanacearum. Current high-throughput DNA sequencing technologies and advances in bioinformatic analyses enable culture-independent approaches to study root-associated microorganisms and their interactions. The structure and dynamics of tobacco root-associated microbiota, as well as functional capacities of certain taxa, may improve how we apply disease management strategies in the field. Through this review we summarize our current understanding on (i) the role of bacterial microbiota on R. solanacearum survival, (ii) the impacts of current management strategies on the soil bacterial communities, (iii) the rhizospheric and core microbiome composition and inheritance, (iv) the manipulation of the microbiota for enhanced disease suppression, and (v) the shortcomings of the application of plant-associated bacteria for disease suppression.

scholarly journals Dynamic Microbiome Changes Reveal the Effect of 1-Methylcyclopropene Treatment on Reducing Post-harvest Fruit Decay in “Doyenne du Comice” Pear

2021 ◽  
Vol 12 ◽  
Author(s):  
Yang Zhang ◽  
Congcong Gao ◽  
Md. Mahidul Islam Masum ◽  
Yudou Cheng ◽  
Chuangqi Wei ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Disease Incidence ◽  
Economic Loss ◽  
Pear Fruit ◽  
Microbial Composition ◽  
Post Harvest ◽  
Control Fruit ◽  
Bacterial Microbiota ◽  
Fruit Decay ◽  
And Control

Pathogen-induced decay is one of the most common causes of fruit loss, resulting in substantial economic loss and posing a health risk to humans. As an ethylene action inhibitor, 1-methylcyclopropene (1-MCP) can significantly reduce fruit decay, but its effect on fruit pathogens remains unclear. Herein, the change in microbial community structure was analyzed using the high-throughput sequencing technology, and characteristics related to fruit quality were determined after 1-MCP (1.0 M l L–1) treatment in “Doyenne du Comiceis” pear fruit during storage at ambient temperature. Overall, 1-MCP was highly effective in reducing disease incidence and induced multiple changes of the fungal and bacterial microbiota. At day 15, the microbial diversity of fungi or bacteria was reduced significantly in the control fruit (non-treated with 1-MCP), which had the most severe decay incidence. For fungi, in addition to Alternaria being the most abundant in both 1-MCP treatment (59.89%) and control (40.18%), the abundances of Botryosphaeria (16.75%), Penicillium (8.81%), and Fusarium (6.47%) increased significantly with the extension of storage time. They became the primary pathogens to cause fruit decay in control, but they were markedly decreased in 1-MCP treatment, resulting in reduced disease incidence. For bacteria, the abundance of Gluconobacter (50.89%) increased dramatically at day 15 in the control fruit, showing that it also played a crucial role in fruit decay. In addition, Botryosphaeria, Fusarium fungi, and Massilia, Kineococcus bacteria were identified as biomarkers to distinguish 1-MCP treatment and control using Random Forest analysis. The redundancy analysis (RDA) result showed that the amount of Botryosphaeria, Penicillium, and Fusarium were positively correlated with disease incidence and respiration rate of pear fruits while negatively correlated with fruit firmness. This investigation is the first comprehensive analysis of the microbiome response to 1-MCP treatment in post-harvest pear fruit, and reveals the relationship between fruit decay and microbial composition in pear fruit.

scholarly journals Ethylene and 1-methylcyclopropene action over senescence of nasturtium flowers

2015 ◽  
Vol 33 (4) ◽  
pp. 453-458 ◽  
Author(s):  
Tania P Silva ◽  
Fernando L Finger
Keyword(s):  
Floral Development ◽  
Development Stage ◽  
Flower Senescence ◽  
Premature Senescence ◽  
Flower Opening ◽  
Development Stages ◽  
Post Harvest ◽  
The Third ◽  
Exogenous Ethylene ◽  
Floral Bud

ABSTRACT: This work describes ethylene and 1-methylcyclopropene (1-MCP) action on post-harvest shelf life of four development stages of nasturtium flowers. To reach this goal, we carried out three experiments. In the first and second experiments, we studied five ethylene (0; 0.1; 1; 10; 100 and 1000 μL/L) and three 1-MCP concentrations (0.25; 0.5 and 0.75 μL/L), respectively. In the third experiment, 1-MCP was followed by combined with ethylene (only 1-MCP; only ethylene; and 24 hours of exposure to 0.75 μL/L 1-MCP followed by 24 hours of exposure to 100 μL/L ethylene). All experiments had two control treatments, one keeping non-exposed flowers inside and another outside exposure chambers. Experiments were set in factorial design, in complete blocks at random, with four 10-flower replications each. Flower senescence was determined by a pre-established visual scale and by observing floral bud development. Ethylene dose above 10 μL/L induced flower wilting and premature senescence from the second floral development stage. Furthermore, higher concentrations of exogenous ethylene promoted irregular flower opening and/or morphological abnormalities in opened flowers. 1-MCP effectively extended post-harvest longevity of nasturtium flowers, independent of the concentration and even in the presence of exogenous ethylene.

scholarly journals Combined genomic, transcriptomic, and metabolomic analyses provide insights into chayote (Sechium edule) evolution and fruit development

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Anzhen Fu ◽  
Qing Wang ◽  
Jianlou Mu ◽  
Lili Ma ◽  
Changlong Wen ◽  
...  
Keyword(s):  
Fruit Development ◽  
Repetitive Sequences ◽  
Genetic Research ◽  
Future Research ◽  
Agricultural Crop ◽  
Protein Coding ◽  
Third Generation Sequencing ◽  
Sechium Edule ◽  
Generation Sequencing ◽  
Cucurbitaceae Family

AbstractChayote (Sechium edule) is an agricultural crop in the Cucurbitaceae family that is rich in bioactive components. To enhance genetic research on chayote, we used Nanopore third-generation sequencing combined with Hi–C data to assemble a draft chayote genome. A chromosome-level assembly anchored on 14 chromosomes (N50 contig and scaffold sizes of 8.40 and 46.56 Mb, respectively) estimated the genome size as 606.42 Mb, which is large for the Cucurbitaceae, with 65.94% (401.08 Mb) of the genome comprising repetitive sequences; 28,237 protein-coding genes were predicted. Comparative genome analysis indicated that chayote and snake gourd diverged from sponge gourd and that a whole-genome duplication (WGD) event occurred in chayote at 25 ± 4 Mya. Transcriptional and metabolic analysis revealed genes involved in fruit texture, pigment, flavor, flavonoids, antioxidants, and plant hormones during chayote fruit development. The analysis of the genome, transcriptome, and metabolome provides insights into chayote evolution and lays the groundwork for future research on fruit and tuber development and genetic improvements in chayote.

scholarly journals Inter and intraspecies comparison of the level of selected bacterial phyla in in cattle and sheep based on feces

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Natalia Szeligowska ◽  
Paulina Cholewińska ◽  
Katarzyna Czyż ◽  
Konrad Wojnarowski ◽  
Marzena Janczak
Keyword(s):  
Digestive Tract ◽  
Environmental Conditions ◽  
Genetic Factors ◽  
Disease Symptoms ◽  
Microbiome Composition ◽  
Bacterial Phyla ◽  
As Species ◽  
Individual Host ◽  
Host Effect ◽  
The Individual

Abstract Background The microbiome of the digestive tract of ruminants contains microbial ecosystem that is affected by both environmental and genetic factors. The subject of this study concerns the influence of selected genetic factors, such as species of animals and “host” individual differences on the digestive tract microbiome composition. The results show the core microbiological composition (Firmicutes and Bacteroidetes) of ruminants digestive tract (based on feces) depending on breed and “host”. The Bacteroidetes and Firmicutes phyla are the most abundant in ruminants digestive tract. The aim of the study was to determine the differences prevalence level of Bacteroidetes and Firmicutes phyla in feces of Charolaise cattle and Polish Olkuska Sheep with respect to intra- and inter-species variability. Results The research group in the experiment consisted of animals at the age of 3 months kept in the same environmental conditions – rams of Polish Olkuska Sheep (n = 10) and Charolaise bulls (n = 10). Feces were collected individually from each animal (animals without disease symptoms were selected), living on the same environmental conditions. The analysis of the results in terms of species showed differences in the Firmicutes phylum level and Lactobacillaceae family between rams and bulls. Subsequently, the analysis performed for the “host effect” showed differentiation in the levels of the Bacteroidetes and Firmicutes phyla between individuals in a group and also between the groups. Conclusion The obtained results suggest that, apart from the diet and the environment, the species and the individual host are equally important factors influencing the microbiological composition of the digestive system of ruminants.

scholarly journals Reconstructing Draft Genomes Using Genome Resolved Metagenomics Reveal Arsenic Metabolizing Genes and Secondary Metabolites in Fresh Water Lake in Eastern India

2021 ◽  
Vol 15 ◽  
pp. 117793222110253
Author(s):  
Samrat Ghosh ◽  
Aditya Narayan Sarangi ◽  
Mayuri Mukherjee ◽  
Deeksha Singh ◽  
Madduluri Madhavi ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Winter Season ◽  
Taxonomic Diversity ◽  
Gene Pools ◽  
Eastern Region ◽  
Microbiome Composition ◽  
Bacterial Phyla ◽  
Medium Quality ◽  
Metagenomic Study

Rabindra Sarovar lake is an artificial freshwater lake in the arsenic infested eastern region of India. In this study, using the genome resolved metagenomics approach; we have deciphered the taxonomic diversity as well as the functional insights of the gene pools specific to this region. Initially, a total of 113 Metagenome Assembled Genomes (MAGs) were recovered from the two predominant seasons, that is, rainy (n = 50) and winter (n = 63). After bin refinement and de-replication, 27 MAGs (18 from Winter season and 9 from Rainy season) were reconstructed. These MAGs were either of high-quality (n = 10) or of medium quality (n = 17) that was determined based on genome completeness and contamination. These 27 MAGs spanning across 6 bacterial phyla and the most predominant ones were Proteobacteria, Bacteroidetes, and Cyanobacteria regardless of the season. Functional annotation across the MAGs suggested the existence of all known types of arsenic resistance and metabolism genes. Besides, important secondary metabolites such as zoocin_A, prochlorosin, and microcin were also abundantly present in these genomes. The metagenomic study of this lake provides the first insights into the microbiome composition and functional classification of the gene pools in two predominant seasons. The presence of arsenic metabolism and resistance genes in the recovered genomes is a sign of adaptation of the microbes to the arsenic contamination in this region. The presence of secondary metabolite genes in the lake microbiome has several implications including the potential use of these for the pharmaceutical industry.

RESEARCH OF THE MICROBIOM OF THE GASTROINTESTINAL TRACT OF THE ABERDIN-ANGUS BREED CATTLE

2021 ◽  
Author(s):  
А.Т. ДАУГАЛИЕВА ◽  
С.Т. ДАУГАЛИЕВА ◽  
Б.С. АРЫНГАЗИЕВ ◽  
Т.А. ЛАВРЕНТЬЕВА
Keyword(s):  
Genetic Identification ◽  
Intestinal Microbiome ◽  
Taxonomic Structure ◽  
Sequencing Technology ◽  
Microbial Composition ◽  
Angus Cattle ◽  
Taxonomic Profile ◽  
New Generation Sequencing ◽  
New Generation ◽  
Generation Sequencing

Целью исследования было определение таксономической структуры микробиома кишечника крупного рогатого скота породы Абердин-Ангус с помощью технологии секвенирования нового поколения. 16S метагеномный анализ, позволил определить микробный состав содержимого кишечника, минуя стадию культивирования на питательных средах. Проведена генетическая идентификация и получен таксономический профиль всех присутствующих бактерий, в том числе и некультивируемых форм. The aim of the study was to determine the taxonomic structure of the intestinal microbiome of Aberdeen Angus cattle using a new generation sequencing technology. 16S metagenomic analysis made it possible to determine the microbial composition of the intestinal contents bypassing the stage of cultivation on nutrient media. Genetic identification was carried out and a taxonomic profile of all bacteria present, including non-cultivated forms, was obtained. Key words: microbiome, cattle, Aberdeen Angus, next generation sequencing.

scholarly journals Lateralized and Segmental Overgrowth in Children

Cancers ◽  
2021 ◽  
Vol 13 (24) ◽  
pp. 6166
Author(s):  
Alessandro Mussa ◽  
Diana Carli ◽  
Simona Cardaropoli ◽  
Giovanni Battista Ferrero ◽  
Nicoletta Resta
Keyword(s):  
Molecular Mechanisms ◽  
Management Strategies ◽  
Tissue Growth ◽  
Body Region ◽  
Molecular Defects ◽  
Embryonic Tissues ◽  
Cellular Signaling Pathway ◽  
Segmental Overgrowth ◽  
Generation Sequencing ◽  
Specific Management

Congenital disorders of lateralized or segmental overgrowth (LO) are heterogeneous conditions with increased tissue growth in a body region. LO can affect every region, be localized or extensive, involve one or several embryonic tissues, showing variable severity, from mild forms with minor body asymmetry to severe ones with progressive tissue growth and related relevant complications. Recently, next-generation sequencing approaches have increased the knowledge on the molecular defects in LO, allowing classifying them based on the deranged cellular signaling pathway. LO is caused by either genetic or epigenetic somatic anomalies affecting cell proliferation. Most LOs are classifiable in the Beckwith–Wiedemann spectrum (BWSp), PI3KCA/AKT-related overgrowth spectrum (PROS/AROS), mosaic RASopathies, PTEN Hamartoma Tumor Syndrome, mosaic activating variants in angiogenesis pathways, and isolated LO (ILO). These disorders overlap over common phenotypes, making their appraisal and distinction challenging. The latter is crucial, as specific management strategies are key: some LO is associated with increased cancer risk making imperative tumor screening since childhood. Interestingly, some LO shares molecular mechanisms with cancer: recent advances in tumor biological pathway druggability and growth downregulation offer new avenues for the treatment of the most severe and complicated LO.

Sign in / Sign up

Export Citation Format

Share Document