scholarly journals Predominant Microbial Colonizers in the Root Endosphere and Rhizosphere of Turfgrass Systems: Pseudomonas veronii, Janthinobacterium lividum, and Pseudogymnoascus spp.

2021 ◽  
Vol 12 ◽  
Author(s):  
Qing Xia ◽  
Thomas Rufty ◽  
Wei Shi
Keyword(s):  
High Throughput Sequencing ◽  
Marker Gene ◽  
Limited Resource ◽  
Creeping Bentgrass ◽  
Fungal Species ◽  
Bulk Soil ◽  
Microbiome Composition ◽  
Janthinobacterium Lividum ◽  
Pseudomonas Veronii ◽  
Ultradwarf Bermudagrass

Microbes can colonize plant roots to modulate plant health and environmental fitness. Thus, using microbes to improve plant adaptation to biotic and abiotic stresses will be promising to abate the heavy reliance of management systems on synthetic chemicals and limited resource. This is particularly important for turfgrass systems because intensive management for plant available nutrients (e.g., nitrogen), water, and pest control is necessary to maintain a healthy and aesthetic landscape. However, little is known on microbial species and host compatibility in turfgrass root endosphere and rhizosphere. Here, by using marker gene high throughput sequencing approaches we demonstrated that a few bacterial and fungal species prevailed the root endosphere and rhizosphere and were of a broad host spectrum. Irrespective of turfgrass species (bermudagrass, ultradwarf bermudagrass, creeping bentgrass, and tall fescue), defoliation intensities (i.e., mowing height and frequency), turfgrass sites, and sampling time, Pseudomonas veronii was predominant in the root endosphere, constituting ∼38% of the total bacterial community, which was much higher than its presence in the bulk soil (∼0.5%) and rhizosphere (∼4.6%). By contrast, Janthinobacterium lividum and fungal species of the genus Pseudogymnoascus were more abundant in the rhizosphere, constituting ∼15 and ∼ 39% of the total bacterial and fungal community, respectively, compared to their respective presence in the bulk soil (∼ 0.1 and 5%) and root endosphere (∼ 0.8 and 0.3%). Such stark contrasts in the microbiome composition between the root endosphere, rhizosphere, and bulk soil were little influenced by turfgrass species, suggesting the broad turfgrass host compatibility of these bacterial and fungal species. Further, their dominance in respective niches were mutually unaffected, implying the possibility of developing a multiple species formula for coping turfgrass with environmental stresses. These species were likely involved in controlling pests, such as infectious nematodes and fungi, decomposing root debris, and helping turfgrass water and nutrient uptake; yet these possibilities need to be further examined.

scholarly journals Different Amplicon Targets for Sequencing-Based Studies of Fungal Diversity

2017 ◽  
Vol 83 (17) ◽  
Author(s):  
Francesca De Filippis ◽  
Manolo Laiola ◽  
Giuseppe Blaiotta ◽  
Danilo Ercolini
Keyword(s):  
Microbial Ecology ◽  
High Throughput ◽  
Biological Samples ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Amplicon Sequencing ◽  
Fungal Species ◽  
Fungal Communities ◽  
Its2 Region ◽  
Mock Community

ABSTRACT Target-gene amplicon sequencing is the most exploited high-throughput sequencing application in microbial ecology. The targets are taxonomically relevant genes, with 16S rRNA being the gold standard for bacteria. As for fungi, the most commonly used target is the internal transcribed spacer (ITS). However, the uneven ITS length among species may promote preferential amplification and sequencing and incorrect estimation of their abundance. Therefore, the use of different targets is desirable. We evaluated the use of three different target amplicons for the characterization of fungal diversity. After an in silico primer evaluation, we compared three amplicons (the ITS1-ITS2 region [ITS1-2], 18S ribosomal small subunit RNA, and the D1/D2 domain of the 26S ribosomal large subunit RNA), using biological samples and a mock community of common fungal species. All three targets allowed for accurate identification of the species present. Nevertheless, high heterogeneity in ITS1-2 length was found, and this caused an overestimation of the abundance of species with a shorter ITS, while both 18S and 26S amplicons allowed for more reliable quantification. We demonstrated that ITS1-2 amplicon sequencing, although widely used, may lead to an incorrect evaluation of fungal communities, and efforts should be made to promote the use of different targets in sequencing-based microbial ecology studies. IMPORTANCE Amplicon-sequencing approaches for fungi may rely on different targets affecting the diversity and abundance of the fungal species. An increasing number of studies will address fungal diversity by high-throughput amplicon sequencing. The description of the communities must be accurate and reliable in order to draw useful insights and to address both ecological and biological questions. By analyzing a mock community and several biological samples, we demonstrate that using different amplicon targets may change the results of fungal microbiota analysis, and we highlight how a careful choice of the target is fundamental for a thorough description of the fungal communities.

scholarly journals Taxonomic Compositions and Co-occurrence Relationships of Protists in Bulk Soil and Rhizosphere of Soybean Fields in Different Regions of China

2021 ◽  
Vol 12 ◽  
Author(s):  
Jun Zhang ◽  
Pengcheng Xing ◽  
Mengyu Niu ◽  
Gehong Wei ◽  
Peng Shi
Keyword(s):  
High Throughput Sequencing ◽  
Niche Overlap ◽  
Spatial Location ◽  
Bulk Soil ◽  
Community Structures ◽  
Potential Predator ◽  
Predator Prey ◽  
Soybean Plants ◽  
Bacteria And Fungi ◽  
Potential Interactions

As the main consumers of bacteria and fungi in farmed soils, protists remain poorly understood. The aim of this study was to explore protist community assembly and ecological roles in soybean fields. Here, we investigated differences in protist communities using high-throughput sequencing and their inferred potential interactions with bacteria and fungi between the bulk soil and rhizosphere compartments of three soybean cultivars collected from six ecological regions in China. Distinct protist community structures characterized the bulk soil and rhizosphere of soybean plants. A significantly higher relative abundance of phagotrophs was observed in the rhizosphere (25.1%) than in the bulk soil (11.3%). Spatial location (R2 = 0.37–0.51) explained more of the variation in protist community structures of soybean fields than either the compartment (R2 = 0.08–0.09) or cultivar type (R2 = 0.02–0.03). The rhizosphere protist network (76 nodes and 414 edges) was smaller and less complex than the bulk soil network (147 nodes and 880 edges), indicating a smaller potential of niche overlap and interactions in the rhizosphere due to the increased resources in the rhizosphere. Furthermore, more inferred potential predator-prey interactions occur in the rhizosphere. We conclude that protists have a crucial ecological role to play as an integral part of microbial co-occurrence networks in soybean fields.

scholarly journals Fungal Community Analysis and Biodeterioration of Waterlogged Wooden Lacquerware from the Nanhai No. 1 Shipwreck

2020 ◽  
Vol 10 (11) ◽  
pp. 3797
Author(s):  
Yin Jia ◽  
Liuyu Yin ◽  
Fengyu Zhang ◽  
Mei Wang ◽  
Mingliang Sun ◽  
...  
Keyword(s):  
Fusarium Solani ◽  
High Throughput Sequencing ◽  
Environmental Parameters ◽  
Community Analysis ◽  
Fungal Species ◽  
Potato Dextrose Agar ◽  
Fungal Communities ◽  
Cellulolytic Enzymes ◽  
Biocidal Products

To avoid the lacquerware of the Nanhai No. 1 shipwreck from being corroded by microorganisms and to improve the knowledge on microbial ecology of the wood lacquers, we conducted a series of tests on the two water samples storing the lacquerware and colonies on the surface of the lacquerware. The high-throughput sequencing detected dominant fungal communities. After that, the fungal strains were isolated and then identified by amplification of ITS- 18S rRNA. Then the activity of ligninolytic and cellulolytic enzymes was detected on potato dextrose agar (PDA) plates with 0.04% (v/v) guaiacol and carboxymethyl cellulose (CMC) agar plates. Finally, we tested the biocide susceptibility of these fungi. Penicillium chrysogenum (NK-NH3) and Fusarium solani (NK- NH1) were the dominant fungi in the sample collected in April 2016 and June 2017. What is more, both showed activity of ligninolytic and cellulolytic enzymes. Four biocidal products (Preventol® D7, P91, BIT 20N, and Euxyl® K100) inhibited the growth of the fungal species in vitro effectively. In further research, the microbial community and environmental parameters in the museum should be monitored to assess the changes in the community and to detect potential microbial outbreaks.

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 Delivery mode and perinatal antibiotics influence the predicted metabolic pathways of the gut microbiome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Petri Vänni ◽  
Mysore V. Tejesvi ◽  
Sofia Ainonen ◽  
Marjo Renko ◽  
Katja Korpela ◽  
...  
Keyword(s):  
Caesarean Section ◽  
Gut Microbiome ◽  
Biological Effects ◽  
Marker Gene ◽  
Delivery Mode ◽  
16S Sequencing ◽  
Microbiome Composition ◽  
Carbohydrate Degradation ◽  
Functional Profiles ◽  
Learning Analysis

AbstractDelivery mode and perinatal antibiotics influence gut microbiome composition in children. Most microbiome studies have used the sequencing of the bacterial 16S marker gene but have not reported the metabolic function of the gut microbiome, which may mediate biological effects on the host. Here, we used the PICRUSt2 bioinformatics tool to predict the functional profiles of the gut microbiome based on 16S sequencing in two child cohorts. Both Caesarean section and perinatal antibiotics markedly influenced the functional profiles of the gut microbiome at the age of 1 year. In machine learning analysis, bacterial fatty acid, phospholipid, and biotin biosynthesis were the most important pathways that differed according to delivery mode. Proteinogenic amino acid biosynthesis, carbohydrate degradation, pyrimidine deoxyribonucleotide and biotin biosynthesis were the most important pathways differing according to antibiotic exposure. Our study shows that both Caesarean section and perinatal antibiotics markedly influence the predicted metabolic profiles of the gut microbiome at the age of 1 year.

scholarly journals Early Stage Root-Associated Fungi Show a High Temporal Turnover, but Are Independent of Beech Progeny

2020 ◽  
Vol 8 (2) ◽  
pp. 210 ◽  
Author(s):  
Kezia Goldmann ◽  
Silke Ammerschubert ◽  
Rodica Pena ◽  
Andrea Polle ◽  
Bin-Wei Wu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Early Stage ◽  
European Beech ◽  
Fungal Species ◽  
Fungal Communities ◽  
Transplant Experiment ◽  
Fungal Community Structure ◽  
Temporal Turnover ◽  
One Year ◽  
The Impact

The relationship between trees and root-associated fungal communities is complex. By specific root deposits and other signal cues, different tree species are able to attract divergent sets of fungal species. Plant intraspecific differences can lead to variable fungal patterns in the root’s proximity. Therefore, within the Beech Transplant Experiment, we analyzed the impact of three different European beech ecotypes on the fungal communities in roots and the surrounding rhizosphere soil at two time points. Beech nuts were collected in three German sites in 2011. After one year, seedlings of the different progenies were out-planted on one site and eventually re-sampled in 2014 and 2017. We applied high-throughput sequencing of the fungal ITS2 to determine the correlation between tree progeny, a possible home-field advantage, plant development and root-associated fungal guilds under field conditions. Our result showed no effect of beech progeny on either fungal OTU richness or fungal community structure. However, over time the fungal OTU richness in roots increased and the fungal communities changed significantly, also in rhizosphere. In both plant compartments, the fungal communities displayed a high temporal turnover, indicating a permanent development and functional adaption of the root mycobiome of young beeches.

scholarly journals Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing

2016 ◽  
Vol 82 (24) ◽  
pp. 7217-7226 ◽  
Author(s):  
D. Lee Taylor ◽  
William A. Walters ◽  
Niall J. Lennon ◽  
James Bochicchio ◽  
Andrew Krohn ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Large Subunit ◽  
Marker Gene ◽  
Soil Samples ◽  
Gene Copy ◽  
Accurate Estimation ◽  
Rrna Gene ◽  
Data Set ◽  
Mock Communities

ABSTRACTWhile high-throughput sequencing methods are revolutionizing fungal ecology, recovering accurate estimates of species richness and abundance has proven elusive. We sought to design internal transcribed spacer (ITS) primers and an Illumina protocol that would maximize coverage of the kingdom Fungi while minimizing nontarget eukaryotes. We inspected alignments of the 5.8S and large subunit (LSU) ribosomal genes and evaluated potential primers using PrimerProspector. We tested the resulting primers using tiered-abundance mock communities and five previously characterized soil samples. We recovered operational taxonomic units (OTUs) belonging to all 8 members in both mock communities, despite DNA abundances spanning 3 orders of magnitude. The expected and observed read counts were strongly correlated (r= 0.94 to 0.97). However, several taxa were consistently over- or underrepresented, likely due to variation in rRNA gene copy numbers. The Illumina data resulted in clustering of soil samples identical to that obtained with Sanger sequence clone library data using different primers. Furthermore, the two methods produced distance matrices with a Mantel correlation of 0.92. Nonfungal sequences comprised less than 0.5% of the soil data set, with most attributable to vascular plants. Our results suggest that high-throughput methods can produce fairly accurate estimates of fungal abundances in complex communities. Further improvements might be achieved through corrections for rRNA copy number and utilization of standardized mock communities.IMPORTANCEFungi play numerous important roles in the environment. Improvements in sequencing methods are providing revolutionary insights into fungal biodiversity, yet accurate estimates of the number of fungal species (i.e., richness) and their relative abundances in an environmental sample (e.g., soil, roots, water, etc.) remain difficult to obtain. We present improved methods for high-throughput Illumina sequencing of the species-diagnostic fungal ribosomal marker gene that improve the accuracy of richness and abundance estimates. The improvements include new PCR primers and library preparation, validation using a known mock community, and bioinformatic parameter tuning.

scholarly journals MiCoP: Microbial Community Profiling method for detecting viral and fungal organisms in metagenomic samples

2018 ◽  
Author(s):  
Nathan LaPierre ◽  
Serghei Mangul ◽  
Mohammed Alser ◽  
Igor Mandric ◽  
Nicholas C. Wu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Human Microbiome ◽  
Real Data ◽  
Human Microbiome Project ◽  
Direct Analysis ◽  
Fungal Species ◽  
Reference Database ◽  
Marker Genes ◽  
Full Diversity ◽  
Community Profiling

AbstractBackgroundHigh throughput sequencing has spurred the development of metagenomics, which involves the direct analysis of microbial communities in various environments such as soil, ocean water, and the human body. Many existing methods based on marker genes or k-mers have limited sensitivity or are too computationally demanding for many users. Additionally, most work in metagenomics has focused on bacteria and archaea, neglecting to study other key microbes such as viruses and eukaryotes.ResultsHere we present a method, MiCoP (Microbiome Community Profiling), that uses fast-mapping of reads to build a comprehensive reference database of full genomes from viruses and eukaryotes to achieve maximum read usage and enable the analysis of the virome and eukaryome in each sample. We demonstrate that mapping of metagenomic reads is feasible for the smaller viral and eukaryotic reference databases. We show that our method is accurate on simulated and mock community data and identifies many more viral and fungal species than previously-reported results on real data from the Human Microbiome Project.ConclusionsMiCoP is a mapping-based method that proves more effective than existing methods at abundance profiling of viruses and eukaryotes in metagenomic samples. MiCoP can be used to detect the full diversity of these communities. The code, data, and documentation is publicly available on GitHub at: https://github.com/smangul1/MiCoP

scholarly journals Dysbiosis of gut microbiota and its correlation with dysregulation of cytokines in psoriasis patients

2021 ◽  
Author(s):  
Xinyue Zhang ◽  
Kun Guo ◽  
Linjing Shi ◽  
Ting Sun ◽  
Songmei Geng
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
High Throughput Sequencing ◽  
Interleukin 2 ◽  
Negative Relationship ◽  
Healthy Individuals ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
The Relationship

Abstract Background: Psoriasis is an inflammatory skin disease associated with multiple comorbidities and substantially diminishes patients’ quality of life. The gut microbiome has become a hot topic in psoriasis as it has been shown to affect both allergy and autoimmunity diseases in recent studies. Our objective was to identify differences in the fecal microbial composition of patients with psoriasis compared with healthy individuals to unravel the microbiota profiling in this autoimmune disease.Results: We collected fecal samples from 30 psoriasis patients and 30 healthy controls, sequenced them by 16S rRNA high-throughput sequencing, and identified the gut microbial composition using bioinformatic analyses including Quantitative Insights into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Our results showed that different relative abundance of certain bacterial taxa between psoriasis patients and healthy individuals, including Faecalibacterium and Megamonas, were increased in patients with psoriasis. It’s also implicated that many cytokines act as main effect molecules in the pathology of psoriasis. We selected the inflammation-related indicators that were abnormal in psoriasis patients and found the microbiome variations were associated with the level of them, especially interleukin-2 receptor showed a positive relationship with Phascolarctobacterium and a negative relationship with the dialister. The relative abundance of Phascolarctobacterium and dialister can be regard as predictors of psoriasis activity. The correlation analysis based on microbiota and Inflammation-related indicators showed that microbiota dysbiosis might induce an abnormal immune response in psoriasis. Conclusions: We concluded that the gut microbiome composition in psoriasis patients has been altered markedly and provides evidence to understand the relationship between gut microbiota and psoriasis. More mechanistic experiments are needed to determine whether the differences observed in gut microbiota are the cause or consequences of psoriasis and whether the relationship between gut microbiota and cytokines was involved.

scholarly journals Microbiome Analysis Exploring Taxonomic Diversity in Kasaragod Dwarf and Holstein Crossbred Cattle

2021 ◽  
Author(s):  
Deepthi M ◽  
Kumar Arvind ◽  
Rituja Saxena ◽  
Joby Pulikkan ◽  
Vineet K Sharma ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Marker Gene ◽  
Taxonomic Diversity ◽  
Crossbred Cattle ◽  
Microbial Composition ◽  
Indigenous Cattle ◽  
Animal Products ◽  
Unifrac Distance ◽  
Unweighted Unifrac ◽  
Principle Coordinate Analysis

Abstract The indigenous cattle are efficient in converting low quality feeds and forage into animal products. Kasaragod Dwarf cattle, a unique non-descriptive native cattle of Kerala, India, are noted for their unique qualities, such as low feed intake, thermotolerance, greater resistance to diseases and A2 allelic variant milk. However, owing to the higher milk yield, Holstein crossbred cattle are given more importance over Kasaragod Dwarf. The hindgut microbiota plays a major role in various biological processes such as the digestion, vitamins synthesis, and immunity in cattle. In this study, we compared the hindgut microbiota of the Kasaragod Dwarf with the highly found, Holstein crossbred utilizing 16S rRNA high-throughput sequencing for a better understanding of the relationship between the host and microbial community. Four replicates of each 20 samples comprising two cattle type (n=10) were sequenced and analyzed. Marker gene-based taxonomic analysis affirmed variations in their microbial composition. Principle Coordinate Analysis (PCoA) using weighted and unweighted UniFrac distance matrices showed the distinct microbial architecture of the two cattle type. Random Forest analysis further confirmed the distinctness and revealed the signature taxa in K-Dwarf. The study observed the predominance of feed efficiency associated genera viz., Anaerovibrio, Succinivibrio, Roseburia, Coprococcus, Anaerostipes, Paludibacter, Elusimicrobium, Sutterella, Oribacterium, Coprobacillus, and Ruminobacter in Kasaragod Dwarf cattle. The study highlights the abundance of unique and beneficial hindgut microflora found in Kasaragod Dwarf, which may attest its importance over exotic cattle breeds viz., Holstein. To our knowledge, this is the first report of Kasaragod Dwarf cattle gut microbiome profiling. This study is pivotal towards developing genetic resources for the microbial population in K-Dwarf and how it could be differentiated from Holstein crossbred cattle.

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