scholarly journals Amplicon-Based Analysis of the Fungal Diversity Across Kenyan Soda Lakes

2021 ◽  
Author(s):  
Romano Mwirichia
Keyword(s):  
Fungal Diversity ◽  
454 Pyrosequencing ◽  
Soda Lakes ◽  
Extreme Environments ◽  
Community Diversity ◽  
Operational Taxonomic Units ◽  
Incertae Sedis ◽  
Physiology And Biochemistry ◽  
Blastn Analysis ◽  
Pyrosequencing Technology

Abstract BackgroundMicroorganisms have been able colonize and thrive in environments characterized by low/high pH, temperature, salt or pressure. Examples of extreme environments are the soda lakes and soda deserts. The objective of this study was to explore the fungal diversity across soda lakes Magadi, Elmenteita, Sonachi and Bogoria in Kenya. A new set of primers was designed to amplify a fragment long enough for the 454-pyrosequencing technology. Results Analysis of the amplicons generated showed that the new primers amplified for eukaryotic groups. A total of 153,634 quality-filtered, non-chimeric sequences were used for community diversity analysis. The sequence reads were clustered into 502 operational taxonomic Units (OTUs) at 97% similarity using BLASTn analysis of which 432 were affiliated to known fungal phylotypes and the rest to other eukaryotes. Fungal OTUs were distributed across 107 genera affiliated to the phylum Ascomycota, Basidiomycota, Glomeromycotina and Incertae Sedis. The Phylum Ascomycota was the most abundant phylotype. Overall, fifteen (15) genera (Chaetomium, Monodictys, Arthrinium, Cladosporium, Fusarium, Myrothecium, Phyllosticta, Coniochaeta, Diatrype, Sarocladium, Sclerotinia, Aspergillus, Preussia and Eutypa) accounted for 65.3% of all the reads. The Genus Cladosporium was detected across all the samples at varying percentages with the highest being water from Lake Bogoria (51.4%). Good’s coverage estimator values ranged between 97 and 100%, an indication that the dominant phylotypes were represented in the data. ConclusionThese results provide useful insights that can guide cultivation dependent studies in order to understand the physiology and biochemistry of the as yet uncultured taxa.

scholarly journals Pyrosequencing Reveals Fungal Communities in the Rhizosphere of Xinjiang Jujube

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Peng Liu ◽  
Xiao-Hui Wang ◽  
Jian-Gui Li ◽  
Wei Qin ◽  
Cheng-Ze Xiao ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Fungal Diversity ◽  
Community Diversity ◽  
Fungal Communities ◽  
Future Research ◽  
Biogeochemical Processes ◽  
Operational Taxonomic Units ◽  
Sequencing Technologies ◽  
Soil Components ◽  
Index Of Diversity

Fungi are important soil components as both decomposers and plant symbionts and play a major role in ecological and biogeochemical processes. However, little is known about the richness and structure of fungal communities. DNA sequencing technologies allow for the direct estimation of microbial community diversity, avoiding culture-based biases. We therefore used 454 pyrosequencing to investigate the fungal communities in the rhizosphere of Xinjiang jujube. We obtained no less than 40,488 internal transcribed spacer (ITS) rDNA reads, the number of each sample was 6943, 6647, 6584, 6550, 6860, and 6904, and we used bioinformatics and multivariate statistics to analyze the results. The index of diversity showed greater richness in the rhizosphere fungal community of a 3-year-old jujube than in that of an 8-year-old jujube. Most operational taxonomic units belonged to Ascomycota, and taxonomic analyses identified Hypocreales as the dominant fungal order. Our results demonstrated that the fungal orders are present in different proportions in different sampling areas. Redundancy analysis (RDA) revealed a significant correlation between soil properties and the abundance of fungal phyla. Our results indicated lower fungal diversity in the rhizosphere of Xinjiang jujube than that reported in other studies, and we hope our findings provide a reference for future research.

scholarly journals Impact of seasonal changes on fungal diversity of a semi-arid ecosystem revealed by 454 pyrosequencing

2015 ◽  
Vol 91 (5) ◽  
Author(s):  
Lluvia Vargas-Gastélum ◽  
Adriana L. Romero-Olivares ◽  
Ana E. Escalante ◽  
Axayácatl Rocha-Olivares ◽  
Carlos Brizuela ◽  
...  
Keyword(s):  
Seasonal Changes ◽  
Fungal Diversity ◽  
454 Pyrosequencing ◽  
Arid Ecosystem ◽  
Semi Arid

scholarly journals Molecular diversity of bacteria in commercially available “Spirulina” food supplements

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1610 ◽  
Author(s):  
Elisabeth Vardaka ◽  
Konstantinos A. Kormas ◽  
Matina Katsiapi ◽  
Savvas Genitsaris ◽  
Maria Moustaka-Gouni
Keyword(s):  
Natural Product ◽  
454 Pyrosequencing ◽  
Molecular Diversity ◽  
Arthrospira Platensis ◽  
Food Supplements ◽  
Health Issues ◽  
Operational Taxonomic Units ◽  
Health Promoting ◽  
First Time ◽  
Pyrosequencing Analysis

The cyanobacteriumArthrospirais among the most well-known food supplements worldwide known as “Spirulina.” While it is a widely recognized health-promoting natural product, there are no reports on the molecular diversity of commercially available brands of “Spirulina” supplements and the occurrence of other cyanobacterial and heterotrophic bacterial microorganisms in these products. In this study, 454-pyrosequencing analysis of the total bacterial occurrence in 31 brands of “Spirulina” dietary supplements from the Greek market was applied for the first time. In all samples, operational taxonomic units (OTUs) ofArthrospira platensiswere the predominant cyanobacteria. Some products contained additional cyanobacterial OTUs including a few known potentially toxic taxa. Moreover, 469 OTUs were detected in all 31 products collectively, with most of them being related to the Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Verrucomicrobia. All samples included heterotrophic bacterial OTUs, ranging from 9–157 per product. Among the most common OTUs were ones closely related to taxa known for causing health issues (i.e.,Pseudomonas,Flavobacterium,Vibrio,Aeromonas,Clostridium,Bacillus,Fusobacterium,Enterococcus). The observed high cyanobacterial and heterotrophic bacterial OTUs richness in the final product is a point for further research on the growth and processing ofArthrospirabiomass for commercial purposes.

scholarly journals Responses of Rhizosphere Fungal Communities to the Sewage Sludge Application into the Soil

2019 ◽  
Vol 7 (11) ◽  
pp. 505 ◽  
Author(s):  
Katarína Ondreičková ◽  
Marcela Gubišová ◽  
Michaela Piliarová ◽  
Miroslav Horník ◽  
Pavel Matušinský ◽  
...  
Keyword(s):  
Sewage Sludge ◽  
Fungal Community ◽  
18S Rdna ◽  
Mycorrhizal Fungi ◽  
Fungal Diversity ◽  
Municipal Wastewater ◽  
Environmental Changes ◽  
Community Diversity ◽  
Rdna Sequencing ◽  
Sludge Application

Due to the increasing sewage sludge production in the world and problems with its disposal, an application of sludge to the soil appears to be a suitable solution considering its fertilizer properties and ability to improve the soil physical conditions. On the other hand, the sludge may also contain undesirable and toxic substances. Since soil microorganisms are sensitive to environmental changes, they can be used as indicators of soil quality. In this study, we used sewage sludge (SS) from two municipal wastewater treatment plants (SS-A and SS-B) in the dose of 5 t/ha and 15 t/ha in order to determine possible changes in the fungal community diversity, especially arbuscular mycorrhizal fungi (AMF), in the rhizosphere of Arundo donax L. Rhizosphere samples were collected in summer and autumn for two consecutive years and the fungal diversity was examined using terminal restriction fragment length polymorphism and 18S rDNA sequencing. Fungal alpha diversity was more affected by SS-A than SS-B probably due to the higher heavy metal content. However, based on principal component analysis and ANOSIM, significant changes in overall fungal diversity were not observed. Simultaneously, 18S rDNA sequencing showed that more various fungal taxa were detected in the sample with sewage sludge than in the control. Glomus sp. as a representative of AMF was the most represented. Moreover, Funneliformis in both samples and Rhizophagus in control with Septoglomus in the sludge sample were other representatives of AMF. Our results indicate that the short-term sewage sludge application into the soil does not cause a shift in the fungal community composition.

scholarly journals Seed-Associated Fungal Diversity and the Molecular Identification of Fusarium with Potential Threat to Ginseng (Panax ginseng) in China

Plant Disease ◽  
2020 ◽  
Vol 104 (2) ◽  
pp. 330-339 ◽  
Author(s):  
Yi Ming Guan ◽  
Jin Chao Deng ◽  
Ying Ying Ma ◽  
Yu Li ◽  
Ya Yu Zhang
Keyword(s):  
Panax Ginseng ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Fusarium Species ◽  
Fungal Species ◽  
Ginseng Root ◽  
Potential Threat ◽  
Operational Taxonomic Units ◽  
Pathogenicity Tests ◽  
Local Storage

The utility of traditional methods for detecting seed-borne fungi is limited by the fact some fungi are unculturable or difficult to isolate. The seed-borne pathogens affecting Panax ginseng cultivation have not been fully characterized. Seed-borne fungi can be identified based on the high-throughput sequencing of internal transcribed spacer (ITS) amplicons. A hierarchical clustering tree diagram analysis based on operational taxonomic units revealed a relationship between the seed-borne fungi and the region from which the seeds were collected. This study analyzed the fungal diversity on 30 ginseng seed samples from the main ginseng-producing areas of China. The 50 most abundant genera were identified including those responsible for ginseng diseases, Fusarium, Alternaria, Nectria, Coniothyrium, Verticillium, Phoma, and Rhizoctonia. Fusarium species, which are the primary causes of root rot, were detected in all seed samples. The results of a phylogenetic analysis indicated that the seed-borne fungal species originating from the same region were closely related. Fungi on ginseng seeds from eight different regions were divided into eight clades, suggesting they were correlated with the local storage medium. A total of 518 Fusarium isolates were obtained and 10 species identified, all of which can be detrimental to ginseng production. Pathogenicity tests proved that seed-borne Fusarium species can infect ginseng seedlings and 2-year-old ginseng root, with potentially adverse effects on ginseng yield and quality.

scholarly journals The Mycobiota of the Deep Sea: What Omics Can Offer

Life ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 292
Author(s):  
Lluvia Vargas-Gastélum ◽  
Meritxell Riquelme
Keyword(s):  
Deep Sea ◽  
Fungal Diversity ◽  
High Salinity ◽  
Extreme Environments ◽  
Abiotic Conditions ◽  
Culture Independent ◽  
Sequencing Platforms ◽  
Generation Sequencing ◽  
Culture Dependent

The deep sea (>1000 m below sea level) represents one of the most extreme environments of the ocean. Despite exhibiting harsh abiotic conditions such as low temperatures, high hydrostatic pressure, high salinity concentrations, a low input of organic matter, and absence of light, the deep sea encompasses a great fungal diversity. For decades, most knowledge on the fungal diversity of the deep sea was obtained through culture-dependent techniques. More recently, with the latest advances of high-throughput next generation sequencing platforms, there has been a rapid increment in the number of studies using culture-independent techniques. This review brings into the spotlight the progress of the techniques used to assess the diversity and ecological role of the deep-sea mycobiota and provides an overview on how the omics technologies have contributed to gaining knowledge about fungi and their activity in poorly explored marine environments. Finally, current challenges and suggested coordinated efforts to overcome them are discussed.

Bacterial Flora of Dental Periradicular Lesions Analyzed by the 454-Pyrosequencing Technology

2012 ◽  
Vol 38 (11) ◽  
pp. 1484-1488 ◽  
Author(s):  
Mohamed H. Saber ◽  
Karen Schwarzberg ◽  
Faisal A. Alonaizan ◽  
Scott T. Kelley ◽  
Parish P. Sedghizadeh ◽  
...  
Keyword(s):  
454 Pyrosequencing ◽  
Bacterial Flora ◽  
Pyrosequencing Technology

454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity

2009 ◽  
Vol 184 (2) ◽  
pp. 449-456 ◽  
Author(s):  
M. Buée ◽  
M. Reich ◽  
C. Murat ◽  
E. Morin ◽  
R. H. Nilsson ◽  
...  
Keyword(s):  
Forest Soils ◽  
Fungal Diversity ◽  
454 Pyrosequencing
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