scholarly journals Variations in the Community Structure of Fungal Microbiota Associated with Apple Fruit Shaped by Fruit Bagging-Based Practice

2021 ◽  
Vol 7 (9) ◽  
pp. 764
Author(s):  
Punda Khwantongyim ◽  
Somying Wansee ◽  
Xi Lu ◽  
Wei Zhang ◽  
Guangyu Sun
Keyword(s):  
Management Practice ◽  
Agricultural Practices ◽  
Apple Fruit ◽  
Fungal Communities ◽  
Compositional Variation ◽  
Fungal Microbiota ◽  
Abundance And Diversity ◽  
Generation Sequencing ◽  
Fruit Part ◽  
Fruit Bagging

The various fungal communities that adhere to apple fruit are influenced by agricultural practices. However, the effects of fruit bagging-based management practice on the fungal microbiota are still unknown, and little is known about the fungal communities of bagged apple fruit. We conducted a study using apple fruit grown in a conventionally managed orchard where pesticide use is an indispensable practice. Fungal communities were collected from the calyx-end and peel tissues of bagged and unbagged fruit and characterized using barcode-type next-generation sequencing. Fruit bagging had a stronger effect on fungal richness, abundance, and diversity of the fungal microbiota in comparison to non-bagging. In addition, bagging also impacted the compositional variation of the fungal communities inhabiting each fruit part. We observed that fruit bagging had a tendency to maintain ecological equilibrium since Ascomycota and Basidiomycota were more distributed in bagged fruit than in unbagged fruit. These fungal communities consist of beneficial fungi rather than potentially harmful fungi. Approximately 50 dominant taxa were detected in bagged fruit, for example, beneficial genera such as Articulospora, Bullera, Cryptococcus, Dioszegia, Erythrobasidium, and Sporobolomyces, as well as pathogenic genera such as Aureobasidium and Taphrina. These results suggested that fruit bagging could significantly increase fungal richness and promote healthy fungal communities, especially the harmless fungal communities, which might be helpful for protecting fruit from the effects of pathogens. This study provides a foundation for understanding the impacts of bagging-based practice on the associated fungal microbiota.

scholarly journals Diversity of Biodeteriorative Bacterial and Fungal Consortia in Winter and Summer on Historical Sandstone of the Northern Pergola, Museum of King John III’s Palace at Wilanow, Poland

2021 ◽  
Vol 11 (2) ◽  
pp. 620
Author(s):  
Magdalena Dyda ◽  
Agnieszka Laudy ◽  
Przemyslaw Decewicz ◽  
Krzysztof Romaniuk ◽  
Martyna Ciezkowska ◽  
...  
Keyword(s):  
Seasonal Changes ◽  
Microbial Community Composition ◽  
Fungal Communities ◽  
Bacterial Strains ◽  
Microbial Biodiversity ◽  
Acidophilic Bacteria ◽  
Almost All ◽  
Generation Sequencing ◽  
King John

The aim of the presented investigation was to describe seasonal changes of microbial community composition in situ in different biocenoses on historical sandstone of the Northern Pergola in the Museum of King John III’s Palace at Wilanow (Poland). The microbial biodiversity was analyzed by the application of Illumina-based next-generation sequencing methods. The metabarcoding analysis allowed for detecting lichenized fungi taxa with the clear domination of two genera: Lecania and Rhinocladiella. It was also observed that, during winter, the richness of fungal communities increased in the biocenoses dominated by lichens and mosses. The metabarcoding analysis showed 34 bacterial genera, with a clear domination of Sphingomonas spp. across almost all biocenoses. Acidophilic bacteria from Acidobacteriaceae and Acetobacteraceae families were also identified, and the results showed that a significant number of bacterial strains isolated during the summer displayed the ability to acidification in contrast to strains isolated in winter, when a large number of isolates displayed alkalizing activity. Other bacteria capable of nitrogen fixation and hydrocarbon utilization (including aromatic hydrocarbons) as well as halophilic microorganisms were also found. The diversity of organisms in the biofilm ensures its stability throughout the year despite the differences recorded between winter and summer.

scholarly journals Cannabis microbiome sequencing reveals several mycotoxic fungi native to dispensary grade Cannabis flowers

F1000Research ◽  
2016 ◽  
Vol 4 ◽  
pp. 1422 ◽  
Author(s):  
Kevin McKernan ◽  
Jessica Spangler ◽  
Lei Zhang ◽  
Vasisht Tadigotla ◽  
Yvonne Helbert ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Food Safety ◽  
Agricultural Products ◽  
Third Party ◽  
Fungal Communities ◽  
Regulatory Requirement ◽  
Safety Testing ◽  
Food Borne ◽  
Generation Sequencing ◽  
The U.S

The Center for Disease Control estimates 128,000 people in the U.S. are hospitalized annually due to food borne illnesses. This has created a demand for food safety testing targeting the detection of pathogenic mold and bacteria on agricultural products. This risk extends to medicalCannabisand is of particular concern with inhaled, vaporized and even concentratedCannabisproducts.As a result, third party microbial testing has become a regulatory requirement in the medical and recreationalCannabismarkets, yet knowledge of theCannabismicrobiome is limited. Here we describe the first next generation sequencing survey of the fungal communities found in dispensary basedCannabisflowers by ITS2 sequencing, and demonstrate the sensitive detection of several toxigenicPenicilliumandAspergillusspecies, includingP. citrinum and P. paxilli,that were not detected by one or more culture-based methods currently in use for safety testing.

scholarly journals Analysis of the Bacterial and Fungal Community Profiles in Bulk Soil and Rhizospheres of Three Mungbean [Vigna radiata (L.) R. Wilczek] Genotypes through PCR-DGGE

2020 ◽  
Vol 77 ◽  
pp. 1-26
Author(s):  
Anna Mae M. de los Reyes ◽  
Eureka Teresa M. Ocampo ◽  
Ma. Carmina C. Manuel ◽  
Bernadette C. Mendoza
Keyword(s):  
Plant Growth ◽  
Crop Production ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Diversity Index ◽  
Agricultural Practices ◽  
Fungal Communities ◽  
Bulk Soil ◽  
Initial Assessment ◽  
Rhizosphere Effect ◽  
Soil Microbial Diversity

Each plant species is regarded to substantially influence and thus, select for specific rhizosphere microbial populations. This is considered in the exploitation of soil microbial diversity associated with important crops, which has been of interest in modern agricultural practices for sustainable productivity. This study used PCR-DGGE (polymerase chain reaction - denaturing gradient gel electrophoresis) in order to obtain an initial assessment of the bacterial and fungal communities associated in bulk soil and rhizospheres of different mungbean genotypes under natural field conditions. Integrated use of multivariate analysis and diversity index showed plant growth stage as the primary driver of community shifts in both microbial groups while rhizosphere effect was found to be less discrete in fungal communities. On the other hand, genotype effect was not discerned but not inferred to be absent due to possible lack of manifestations of differences among genotypes based on tolerance to drought under non-stressed environment, and due to detection limits of DGGE. Sequence analysis of prominent members further revealed that Bacillus and Arthrobacter species were dominant in bacterial communities whereas members of Ascomycota and Basidiomycota were common in fungal communities of mungbean. Overall, fungal communities had higher estimated diversity and composition heterogeneity, and were more dynamic under plant growth influence, rhizosphere effect and natural environmental conditions during mungbean growth in upland field. These primary evaluations are prerequisite to understanding the interactions between plant and rhizosphere microorganisms with the intention of employing their potential use for sustainable crop production.

scholarly journals InDel assembly: A novel framework for engineering protein loops through length and compositional variation

2017 ◽  
Author(s):  
Pedro A. G. Tizei ◽  
Emma Harris ◽  
Marleen Renders ◽  
Vitor B. Pinheiro
Keyword(s):  
Substrate Specificity ◽  
Building Blocks ◽  
Sequence Length ◽  
Compositional Variation ◽  
Length Variation ◽  
Dna Assembly ◽  
Sequence Composition ◽  
Efficient Route ◽  
Generation Sequencing ◽  
Protein Loops

AbstractInsertions and deletions (indels) are known to affect function, biophysical properties and substrate specificity of enzymes, and they play a central role in evolution. Despite such clear significance, this class of mutation remains an underexploited tool in protein engineering with no available platforms capable of systematically generating or analysing libraries of varying sequence composition and length. We present a novel DNA assembly platform (InDel assembly), based on cycles of endonuclease restriction and ligation of standardised dsDNA building blocks, that can generate libraries exploring both composition and sequence length variation. In addition, we developed a framework to analyse the output of selection from InDel-generated libraries, combining next generation sequencing and alignment-free strategies for sequence analysis. We demonstrate the approach by engineering the well-characterized TEM-1 β-lactamase Ω-loop, involved in substrate specificity, identifying multiple novel extended spectrum β-lactamases with loops of modified length and composition areas of the sequence space not previously explored. Together, the InDel assembly and analysis platforms provide an efficient route to engineer protein loops or linkers where sequence length and composition are both essential functional parameters.

Abundance and Diversity of CO2-Assimilating Bacteria and Algae Within Red Agricultural Soils Are Modulated by Changing Management Practice

2015 ◽  
Vol 70 (4) ◽  
pp. 971-980 ◽  
Author(s):  
Hongzhao Yuan ◽  
Tida Ge ◽  
Xiangbi Chen ◽  
Shoulong Liu ◽  
Zhenke Zhu ◽  
...  
Keyword(s):  
Agricultural Soils ◽  
Management Practice ◽  
Abundance And Diversity

scholarly journals Mixed-Cropping Between Field Pea Varieties Alters Root Bacterial and Fungal Communities

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Anthony Horner ◽  
Samuel S. Browett ◽  
Rachael E. Antwis
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Crop Production ◽  
Agricultural Soils ◽  
Critical Role ◽  
Agricultural Practices ◽  
Microbial Interactions ◽  
Field Pea ◽  
Fungal Communities ◽  
Mixed Cropping

AbstractModern agricultural practices have vastly increased crop production but negatively affected soil health. As such, there is a call to develop sustainable, ecologically-viable approaches to food production. Mixed-cropping of plant varieties can increase yields, although impacts on plant-associated microbial communities are unclear, despite their critical role in plant health and broader ecosystem function. We investigated how mixed-cropping between two field pea (Pisum sativum L.) varieties (Winfreda and Ambassador) influenced root-associated microbial communities and yield. The two varieties supported significantly different fungal and bacterial communities when grown as mono-crops. Mixed-cropping caused changes in microbial communities but with differences between varieties. Root bacterial communities of Winfreda remained stable in response to mixed-cropping, whereas those of Ambassador became more similar to Winfreda. Conversely, root fungal communities of Ambassador remained stable under mixed-cropping, and those of Winfreda shifted towards the composition of Ambassador. Microbial co-occurrence networks of both varieties were stronger and larger under mixed-cropping, which may improve stability and resilience in agricultural soils. Both varieties produced slightly higher yields under mixed-cropping, although overall Ambassador plants produced higher yields than Winfreda plants. Our results suggest that variety diversification may increase yield and promote microbial interactions.

Long-term effects of stump removal and tree species composition on the diversity and structure of soil fungal communities

2020 ◽  
Vol 96 (5) ◽  
Author(s):  
Dixi Modi ◽  
Suzanne Simard ◽  
Jean Bérubé ◽  
Les Lavkulich ◽  
Richard Hamelin ◽  
...  
Keyword(s):  
Species Composition ◽  
Fungal Community ◽  
Tree Species ◽  
Management Practice ◽  
Tree Regeneration ◽  
Root Disease ◽  
Fungal Communities ◽  
Tree Species Composition ◽  
The Impact

ABSTRACT Stump removal is a common forest management practice used to reduce the mortality of trees affected by the fungal pathogen-mediated root disease, Armillaria root rot, but the impact of stumping on soil fungal community structure is not well understood. This study analyzed the long-term impact of stumping and tree species composition on the abundance, diversity and taxonomic composition of soil fungal communities using internal transcribed spacer (ITS) marker-based DNA metabarcoding in a 48-year-old trial at Skimikin, British Columbia. A total of 108 samples were collected from FH (fermented and humus layers), and soil mineral horizons (A and B) from stumped and unstumped plots of six tree species treatments (pure stands and admixtures of Douglas-fir, western red-cedar and paper birch). Fungal α-diversity in the A horizon significantly increased with stumping regardless of tree species composition, while β-diversity was significantly affected by stumping in all the horizons. We also observed that the relative abundance of the saprotrophic fungal community declined while that of the ectomycorrhizal fungal community increased with stumping. In conclusion, increase in ectomycorrhizal fungal associations, which are positively associated with tree productivity, suggests that stumping can be considered a good management practice for mitigating root disease and promoting tree regeneration.

scholarly journals Fungal communities in barren forest soil after amendment with different wood substrates and their possible effects on trees’, pathogens, insects and nematodes

2015 ◽  
Vol 55 (3) ◽  
pp. 301-311 ◽  
Author(s):  
Monika Małecka ◽  
Hanna Kwaśna ◽  
Wojciech Szewczyk
Keyword(s):  
Forest Soil ◽  
Scots Pine ◽  
Sandy Loam ◽  
Woody Debris ◽  
Fungal Communities ◽  
Dilution Method ◽  
Pine Sawdust ◽  
Post Harvest ◽  
Abundance And Diversity

AbstractScots pine sawdust, composted bark or coarse, post-harvest woody debris from conifers had been spread over the surface of barren forest soil before planting with Scots pine. The effects of the Scots pine sawdust, composted bark or coarse, post-harvest woody debris from conifers on the abundance and diversity of culturable fungi were investigated. The amendments were aimed at increasing the soil suppressiveness toArmillariaandHeterobasidion.The classical soil-dilution method was chosen for qualitative and quantitative analyses of fungal communities in soils because of its proven reliability and consistency. The soil was inhabited by saprotrophic fungi from Ascomycota and Zygomycota, including species known to be potential antagonists ofArmillariaorH. annosum(i.e.Clonostachys + Trichodermaspp.,Penicillium commune, P. daleae,P. janczewskii) or stimulants ofArmillaria(i.e.Pseudogymnoascus roseus,Trichocladium opacum). Eleven years after treatment, the abundance and diversity of fungi, the abundance ofP. commune, and locally the abundance ofP. janczewskiiincreased, whileClonostachys + Trichodermaspp., and locally,P. daleaeandT. opacumdecreased. Amending the barren soil with organic matter does not guarantee effective, long-term suppressiveness of the sandy loam soil toArmillariaandHeterobasidion.Increased abundance of entomopathogenic and nematophagous species, 11 years after treatment, does suggest the long-term possibility of insect or nematode control in soil.

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