scholarly journals Seasonal Characterization of the Endophytic Fungal Microbiome of Mulberry (Morus spp.) Cultivars Resistant and Susceptible to Sclerotiniosis

2021 ◽  
Vol 9 (10) ◽  
pp. 2052
Author(s):  
Weifang Xu ◽  
Fei Wang ◽  
Ruolin Wang ◽  
Yuan Sui ◽  
Zeyang Zhou ◽  
...  
Keyword(s):  
Fruit Production ◽  
Resistance Level ◽  
Operational Taxonomic Units ◽  
Mulberry Fruit ◽  
Α Diversity ◽  
Culture Independent ◽  
Morus Spp ◽  
Fungal Microbiome ◽  
Seasonal Shifts

The endophytic microbiome is thought to play an important role in promoting plant growth and health. Using culture-independent and culture-dependent protocols, this study characterized the seasonal shifts in the endophytic fungal microbiota of four mulberry (Morus L.) cultivars having different levels of resistance to mulberry fruit sclerotiniosis. Core endophytes can be obtained by two approaches, and they were divided into two clusters by season. Spring samples harbored higher operational taxonomic units (OTUs) and α-diversity, while autumn samples had more sequences or isolates of the fungal class Dothideomycetes with the representative orders Capnodiales and Pleosporales. While comparing different mulberry cultivars, we found that the total number of OTUs in susceptible cultivars was higher than that of resistant cultivars, and Cladosporium sp. were observed in all. Notably, the causal agent of fruit sclerotiniosis (Scleromitrula shiraiana) was only detected in susceptible cultivars. Collectively, our work elucidated significant variations in the mulberry endophytic microbiome, mainly because of seasonal shifts, and the fact that the host cultivars and mulberry endophytic fungal community appeared to have a certain connection with the resistance level of mulberry fruit to sclerotiniosis. These results provided valuable information on the isolation and culturing of mulberry endophytes that could be applied to improve mulberry fruit production and health.

scholarly journals New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

2021 ◽  
Vol 9 (3) ◽  
pp. 659
Author(s):  
Elias Asimakis ◽  
Panagiota Stathopoulou ◽  
Apostolis Sapounas ◽  
Kanjana Khaeso ◽  
Costas Batargias ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Mutual Exclusion ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Host Diet ◽  
Dominant Bacteria ◽  
High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

scholarly journals Culture-dependent and culture-independent characterization of microorganisms associated with Aedes aegypti (Diptera: Culicidae) (L.) and dynamics of bacterial colonization in the midgut

Acta Tropica ◽  
2010 ◽  
Vol 115 (3) ◽  
pp. 275-281 ◽  
Author(s):  
Desiely S. Gusmão ◽  
Adão V. Santos ◽  
Danyelle C. Marini ◽  
Mauricio Bacci ◽  
Marília A. Berbert-Molina ◽  
...  
Keyword(s):  
Aedes Aegypti ◽  
Bacterial Colonization ◽  
Culture Independent ◽  
Culture Dependent

Micromorphological Characterization of Ten Mulberry Cultivars (Morus spp)

2004 ◽  
Vol 58 (4) ◽  
pp. 639-646 ◽  
Author(s):  
Magda Biasiolo ◽  
Maria Teresa Da Canal ◽  
Noemi Tornadore
Keyword(s):  
Morus Spp

scholarly journals Viruses and Virus Diseases of Rubus

Plant Disease ◽  
2013 ◽  
Vol 97 (2) ◽  
pp. 168-182 ◽  
Author(s):  
Robert R. Martin ◽  
Stuart MacFarlane ◽  
Sead Sabanadzovic ◽  
Diego Quito ◽  
Bindu Poudel ◽  
...  
Keyword(s):  
Far East ◽  
Fruit Production ◽  
Detection Methods ◽  
Center Of Origin ◽  
The Family ◽  
Production Stages ◽  
Rubus Species ◽  
Polymerase Chain ◽  
Made In

Blackberry and raspberry are members of the family Rosaceae. They are classified in the genus Rubus, which comprises hundreds of species and has a center of origin in the Far East. Rubus is divided into 15 subgenera with blackberries classified in the Rubus (formerly Eubatus) and raspberries in the Idaeobatus subgenera. Rubus species are propagated vegetatively and are subject to infection by viruses during development, propagation, and fruit production stages. Reports of initial detection and symptoms of more than 30 viruses, virus-like diseases, and phytoplasmas affecting Rubus spp. were reviewed more than 20 years ago. Since the last review on Rubus viruses, significant progress has been made in the molecular characterization of many of the viruses that infect Rubus spp. Currently, reverse transcription–polymerase chain reaction detection methods are available for most of the viruses known to infect Rubus. The goals of this article are to update the knowledge on previously characterized viruses of Rubus, highlight recently described viruses, review the virus-induced symptoms, describe the advances made in their detection, and discuss our knowledge about several virus complexes that cause serious diseases in Rubus. Virus complexes have been identified recently as the major cause of diseases in blackberries and raspberries.

scholarly journals Characterization of the gut DNA and RNA viromes in a cohort of Chinese residents and visiting Pakistanis

2020 ◽  
Author(s):  
Qiulong Yan ◽  
Yu Wang ◽  
Xiuli Chen ◽  
Hao Jin ◽  
Guangyang Wang ◽  
...  
Keyword(s):  
Ethnic Origin ◽  
Chinese Adults ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Dna And Rna ◽  
Bacterial Microbiome ◽  
Chinese Cohort ◽  
Host Genetic

AbstractBackgroundTrillions of viruses inhabit the gastrointestinal tract. Some of them have been well-studied on their roles in infection and human health, but the majority remain unsurveyed. It has been established that the composition of the gut virome is highly variable based on the changes of diet, physical state, and environmental factors. However, the effect of host genetic factors, e.g. ethnic origin, on the gut virome is rarely investigated.Methods and ResultsHere, we characterized and compared the gut virome in a cohort of local Chinese residents and visiting Pakistani individuals, each group containing 24 healthy adults and 6 children. Using metagenomic shotgun sequencing and assembly of fecal samples, a huge number of viral operational taxonomic units (vOTUs) were identified for profiling the DNA and RNA viromes. National background contributed a primary variation to individuals’ gut virome. Compared with the Chinese adults, the Pakistan adults showed higher macrodiversity and different compositional and functional structures in their DNA virome and lower diversity and altered composition in their RNA virome. The virome variations of Pakistan children were inherited from the that of the adults but also tended to share similar characteristics with the Chinese cohort. We also analyzed and compared the bacterial microbiome between two cohorts and further revealed numerous connections between virus and bacterial host. Statistically, the gut DNA and RNA viromes were covariant to some extent (p<0.001), and they both influenced the holistic bacterial composition and vice versa.ConclusionsThis study provides an overview of gut viral community in Chinese and visiting Pakistanis and proposes a considerable role of ethnic origin in shaping the virome.

scholarly journals Morphological Characterization of Mulberry (Morus spp.) Accessions Grown in Kenya

2013 ◽  
Vol 3 (1) ◽  
pp. 10 ◽  
Author(s):  
Nderitu Wangari Peris ◽  
Kinyua Mirriam Gacheri ◽  
Mutui Mwendwa Theophillus ◽  
Ngode Lucas
Keyword(s):  
Hierarchical Cluster ◽  
Morphological Characterization ◽  
Phenotypic Traits ◽  
Mulberry Leaf ◽  
Leaf Yield ◽  
Morus Spp ◽  
Positive Correlations ◽  
Internode Distance ◽  
Number Of Branches

<p>Genetic divergence of five mulberry accessions including Embu, Thika, Thailand (<em>M. alba</em>), Kanva-2 and S41 (<em>M. indica</em>) grown in Kenya were examined using twelve phenotypic traits. The assessment of phenotypic traits was done in a field study in two localities, Nairobi and Eldoret. The traits that were significantly different across the mulberry accessions included lamina width and petiole length (P ? 0.01), petiole width and growth height (P ? 0.05), internodes distance and number of branches (P ? 0.001). The Duncan’s Multiple Range Test (DMRT) results were used to generate a dendrogram derived from hierarchical cluster analysis that further partitioned the mulberry accessions into four groups. Embu and Thailand accessions grouped together while S41, Thika and Kanva-2 accessions grouped separately. Embu and Thailand accessions were characterized by fewer numbers of branches than the rest of the accessions. Thika accession had high number of branches and short internode distance. Significant and positive correlations were found between leaf yield traits except in internode distance and number of branches which were significant and negatively correlated. Significant and positive correlations can be utilized since they are rewarding for mulberry leaf yield improvement.</p>

scholarly journals Phylogenetic and Chemical Diversity of a Hybrid-Isoprenoid-Producing Streptomycete Lineage

2013 ◽  
Vol 79 (22) ◽  
pp. 6894-6902 ◽  
Author(s):  
Kelley A. Gallagher ◽  
Kristin Rauscher ◽  
Laura Pavan Ioca ◽  
Paul R. Jensen
Keyword(s):  
Secondary Metabolites ◽  
Secondary Metabolite ◽  
Sequence Data ◽  
Environmental Dna ◽  
Chemical Diversity ◽  
Phenotypic Trait ◽  
Content Type ◽  
Operational Taxonomic Units ◽  
Culture Independent ◽  
Structural Classes

ABSTRACTStreptomycesspecies dedicate a large portion of their genomes to secondary metabolite biosynthesis. A diverse and largely marine-derived lineage within this genus has been designated MAR4 and identified as a prolific source of hybrid isoprenoid (HI) secondary metabolites. These terpenoid-containing compounds are common in nature but rarely observed as bacterial secondary metabolites. To assess the phylogenetic diversity of the MAR4 lineage, complementary culture-based and culture-independent techniques were applied to marine sediment samples collected off the Channel Islands, CA. The results, including those from an analysis of publically available sequence data and strains isolated as part of prior studies, placed 40 new strains in the MAR4 clade, of which 32 originated from marine sources. When combined with sequences cloned from environmental DNA, 28 MAR4 operational taxonomic units (0.01% genetic distance) were identified. Of these, 82% consisted exclusively of either cloned sequences or cultured strains, supporting the complementarity of these two approaches. Chemical analyses of diverse MAR4 strains revealed the production of five different HI structure classes. All 21 MAR4 strains tested produced at least one HI class, with most strains producing from two to four classes. The two major clades within the MAR4 lineage displayed distinct patterns in the structural classes and the number and amount of HIs produced, suggesting a relationship between taxonomy and secondary metabolite production. The production of HI secondary metabolites appears to be a phenotypic trait of the MAR4 lineage, which represents an emerging model with which to study the ecology and evolution of HI biosynthesis.

Paucimyces polynucleatus gen. nov, sp. nov., a novel polycentric genus of anaerobic gut fungi from the faeces of a wild blackbuck antelope

2021 ◽  
Vol 71 (6) ◽  
Author(s):  
Radwa A. Hanafy ◽  
Noha H. Youssef ◽  
Mostafa S. Elshahed
Keyword(s):  
Ribosomal Subunit ◽  
New Genus And Species ◽  
Isolation And Characterization ◽  
Faecal Samples ◽  
Wide Range ◽  
Culture Independent ◽  
Antilope Cervicapra ◽  
Spherical Vesicles ◽  
Sequence Similarities

The anaerobic gut fungi (AGF; phylum Neocallimastigomycota) reside in the alimentary tracts of herbivores. Multiple novel, yet-uncultured AGF taxa have recently been identified in culture-independent diversity surveys. Here, we report on the isolation and characterization of the first representative of the RH5 lineage from faecal samples of a wild blackbuck (Indian Antelope, Antilope cervicapra) from Sutton County, Texas, USA. The isolates displayed medium sized (2–4 mm) compact circular colonies on agar roll tubes and thin loose biofilm-like growth in liquid medium. Microscopic examination revealed monoflagellated zoospores and polycentric thalli with highly branched nucleated filamentous rhizomycelium, a growth pattern encountered in a minority of described AGF genera so far. The obtained isolates are characterized by formation of spherical vesicles at the hyphal tips from which multiple sporangia formed either directly on the spherical vesicles or at the end of sporangiophores. Phylogenetic analysis using the D1/D2 regions of the large ribosomal subunit (D1/D2 LSU) and the ribosomal internal transcribed spacer 1 (ITS1) revealed sequence similarities of 93.5 and 81.3%, respectively, to the closest cultured relatives (Orpinomyces joyonii strain D3A (D1/D2 LSU) and Joblinomyces apicalis strain GFH681 (ITS1). Substrate utilization experiments using the type strain (BB-3T) demonstrated growth capabilities on a wide range of mono-, oligo- and polysaccharides, including glucose, xylose, mannose, fructose, cellobiose, sucrose, maltose, trehalose, lactose, cellulose, xylan, starch and raffinose. We propose accommodating these novel isolates in a new genus and species, for which the name Paucimyces polynucleatus gen. nov., sp. nov. is proposed.

scholarly journals Characterization of fungal and bacterial dysbiosis in young adult Chinese patients with Crohn’s disease

2020 ◽  
Vol 13 ◽  
pp. 175628482097120
Author(s):  
Xinyun Qiu ◽  
Xiaojing Zhao ◽  
Xiufang Cui ◽  
Xiaqiong Mao ◽  
Nana Tang ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Chinese Patients ◽  
Bacterial Composition ◽  
Structural Differences ◽  
Inflammatory Bowel ◽  
Fungal Microbiome ◽  
Chinese Subjects

Intestinal microbiota dysbiosis has been described in inflammatory bowel disease (IBD), but data from China are limited. In this study, we performed molecular analysis of the fecal microbial community from 20 healthy Chinese subjects and 25 patients with Crohn’s disease (CD), and evaluated associations with bacterial and fungal compositions. Decreased richness and diversity of bacterial composition was observed in the CD group compared with healthy (H) subjects. Significant structural differences in bacterial (but not fungal) composition among healthy controls and CD patients were found. A reduction in Firmicutes and Actinobacteria abundance, and overrepresentation of Proteobacteria were observed in the CD patients compared with the H group. The Escherichia-Shigella genus was overrepresented in the CD group, whereas Faecalibacterium, Gemmiger, Bifidobacterium, Romboutsia, Ruminococcus, Roseburia, and Fusicatenibacter abundance were decreased in the CD group compared with H subjects. Differences in fungal microbiota between the H and CD groups were observed at the genus rather than at the phylum level. The Candida genus was overrepresented in the CD (active disease) group compared with the H group, whereas no difference between CD (remission) and H groups was observed. Aspergillus, unclassified_Sordariomycetes, and Penicillium genera had greater representation in the H subjects compared with the CD group. Bacterial and fungal intra- and inter-kingdom correlations were observed between the H and CD groups. Therefore, fecal bacterial and fungal microbiome communities differed considerably between H and CD patients, and between Chinese and Western populations. The role of gut microbiota in homeostasis and in gastrointestinal disorders should be investigated further.

scholarly journals Lactococcus lactis Diversity Revealed by Targeted Amplicon Sequencing of purR Gene, Metabolic Comparisons and Antimicrobial Properties in an Undefined Mixed Starter Culture Used for Soft-Cheese Manufacture

Foods ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 622
Author(s):  
Sabrina Saltaji ◽  
Olivier Rué ◽  
Valérie Sopena ◽  
Sophie Sablé ◽  
Fatoumata Tambadou ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Starter Culture ◽  
Antimicrobial Properties ◽  
Amplicon Sequencing ◽  
Antimicrobial Activities ◽  
Operational Taxonomic Units ◽  
Soft Cheese ◽  
Culture Independent ◽  
Identification Of Species ◽  
Species Specific

The undefined mixed starter culture (UMSC) is used in the manufacture of cheeses. Deciphering UMSC microbial diversity is important to optimize industrial processes. The UMSC was studied using culture-dependent and culture-independent based methods. MALDI-TOF MS enabled identification of species primarily from the Lactococcus genus. Comparisons of carbohydrate metabolism profiles allowed to discriminate five phenotypes of Lactococcus (n = 26/1616). The 16S sequences analysis (V1–V3, V3–V4 regions) clustered the UMSC microbial diversity into two Lactococcus operational taxonomic units (OTUs). These clustering results were improved with the DADA2 algorithm on the housekeeping purR sequences. Five L. lactis variants were detected among the UMSC. The whole-genome sequencing of six isolates allowed for the identification of the lactis subspecies using Illumina® (n = 5) and Pacbio® (n = 1) technologies. Kegg analysis confirmed the L. lactis species-specific niche adaptations and highlighted a progressive gene pseudogenization. Then, agar spot tests and agar well diffusion assays were used to assess UMSC antimicrobial activities. Of note, isolate supernatants (n = 34/1616) were shown to inhibit the growth of Salmonella ser. Typhimurium CIP 104115, Lactobacillus sakei CIP 104494, Staphylococcus aureus DSMZ 13661, Enterococcus faecalis CIP103015 and Listeria innocua CIP 80.11. Collectively, these results provide insightful information about UMSC L. lactis diversity and revealed a potential application as a bio-protective starter culture.

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