Metagenomic analysis of bacterial and fungal community composition associated with Paulownia elongata × Paulownia fortunei

The dynamics and interactions of microbial communities in Paulownia’s life cycle are poorly understood. The main goal of this study was to compare the rhizospheric soil and endophytic microbiome and mycobiome of hybrid Paulownia elongata and Paulownia fortunei. The comparison was based on highly efficient Illumina MiSeq sequencing of bacteria and fungi from the rhizosphere and endosphere of bioenergetic trees P. elongata x P. fortunei. The general richness of bacteria and rhizospheric fungi (based on Chao 1, Shannon, and Simpson indicators) was higher than in endosphere samples from the same plants. Actinobacteria and Proteobacteria were dominant in the rhizosphere and endosphere of plants in healthy conditions. The rhizosphere fungal communities in both trials were dominated by Ascomycota, Mortierellomycota, and Basidiomycota. Most root endophytes came from Olpidiomycota, Oomycota, and Ascomycota, while most leaf endophytes were from Ascomycota and Basidiomycota. This study was the first report on the composition of bacteria and fungi associated with the endosphere and rhizosphere of Paulownia trees. These studies showed that bacterial and fungal communities from the rhizosphere and endosphere were separate communities. It also showed that the health conditions of trees did not affect the composition of endophytic microorganisms in Paulownia tissues.

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Clary Sage Cultivation and Mycorrhizal Inoculation Influence the Rhizosphere Fungal Community of an Aged Trace-Element Polluted Soil

Microorganisms ◽

10.3390/microorganisms9061333 ◽

2021 ◽

Vol 9 (6) ◽

pp. 1333

Author(s):

Robin Raveau ◽

Anissa Lounès-Hadj Sahraoui ◽

Mohamed Hijri ◽

Joël Fontaine

Keyword(s):

Trace Element ◽

Community Composition ◽

Mycorrhizal Fungi ◽

Arbuscular Mycorrhizal ◽

Illumina Miseq ◽

Amplicon Sequencing ◽

Fungal Communities ◽

Rhizospheric Soil ◽

Lead Smelter ◽

Amf Communities

Soil fungal communities play a central role in natural systems and agroecosystems. As such, they have attracted significant research interest. However, the fungal microbiota of aromatic plants, such as clary sage (Salvia sclarea L.), remain unexplored. This is especially the case in trace element (TE)-polluted conditions and within the framework of phytomanagement approaches. The presence of high concentrations of TEs in soils can negatively affect not only microbial diversity and community composition but also plant establishment and growth. Hence, the objective of this study is to investigate the soil fungal and arbuscular mycorrhizal fungi (AMF) community composition and their changes over time in TE-polluted soils in the vicinity of a former lead smelter and under the cultivation of clary sage. We used Illumina MiSeq amplicon sequencing to evaluate the effects of in situ clary sage cultivation over two successive years, combined or not with exogenous AMF inoculation, on the rhizospheric soil and root fungal communities. We obtained 1239 and 569 fungal amplicon sequence variants (ASV), respectively, in the rhizospheric soil and roots of S. sclarea under TE-polluted conditions. Remarkably, 69 AMF species were detected at our experimental site, belonging to 12 AMF genera. Furthermore, the inoculation treatment significantly shaped the fungal communities in soil and increased the number of AMF ASVs in clary sage roots. In addition, clary sage cultivation over successive years could be one of the explanatory parameters for the inter-annual variation in both fungal and AMF communities in the soil and root biotopes. Our data provide new insights on fungal and AMF communities in the rhizospheric soil and roots of an aromatic plant, clary sage, grown in TE-polluted agricultural soil.

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Mudflat reclamation causes change in the composition of fungal communities under long-term rice cultivation

Canadian Journal of Microbiology ◽

10.1139/cjm-2019-0005 ◽

2019 ◽

Vol 65 (7) ◽

pp. 530-537 ◽

Cited By ~ 3

Author(s):

Yang Zhang ◽

Qing Li ◽

Yinglong Chen ◽

Qigen Dai ◽

Jian Hu

Keyword(s):

Soil Fertility ◽

Fungal Community ◽

Critical Role ◽

Illumina Miseq ◽

Rice Cultivation ◽

Fungal Communities ◽

Fungal Community Composition ◽

Saprotrophic Fungi ◽

Factors Affecting

Fungi play a critical role in farmland ecosystems, especially in improving soil fertility; however, little is known about the changes in fungal communities caused by mudflat reclamation under rice cultivation. In this study, mudflats located in Yancheng, China, which were divided into nine plots with 0, 11, and 20 years of successive rice cultivation histories, were sampled to determine the fungal community composition by using Illumina MiSeq sequencing. Results show that the Shannon diversity of the fungal communities did not change significantly but the species richness increased under mudflat reclamation with long-term rice cultivation. Ascomycota was the dominant phylum throughout the reclaimed mudflats samples, while Sordariomycetes was the dominant class. Fungal functional prediction found that the relative abundance of saprotrophs gradually increased with mudflat reclamation and mainly belonged to Ascomycota after 20 years of successive reclamation. Redundancy analysis showed that electrical conductivity, organic matter, and total nitrogen were the main factors affecting the composition and ecological function of the fungal community during mudflat reclamation. In short, a fungal community dominated by Ascomycota was established during mudflat reclamation under rice cultivation, which is more conducive to promoting soil fertility because of the higher proportion of saprotrophic fungi in Ascomycota.

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Contrasting patterns and co-occurrence network of soil bacterial and fungal community along depth profiles in cold temperate montane forests of China

10.1101/2021.04.11.439312 ◽

2021 ◽

Author(s):

Li Ji ◽

Fangyuan Shen ◽

Yue Liu ◽

Yuchun Yang ◽

Jun Wang ◽

...

Keyword(s):

Fungal Community ◽

Soil Depth ◽

Illumina Miseq ◽

Fungal Communities ◽

Fungal Community Composition ◽

Altitudinal Distribution ◽

Core Composition ◽

Key Species ◽

Subsurface Soil ◽

Soil Bacterial

AbstractSoil bacterial and fungal communities with different key ecological functions play an important role in the boreal forest ecosystem. Despite several studies have reported the microbial altitudinal distribution patterns, our understanding about the characteristics of the microbial community and the core composition of the microbiome in cold-temperate mountain forests is still limited. In this study, Illumina MiSeq sequencing was used to investigate the changes in soil bacterial and fungal communities in surface and subsurface soils along at an altitudinal gradient (from 830 m to 1300 m) on Oakley Mountain in the northern Greater Khingan Mountains. Altitude and soil depth had significant impacts on the relative abundance of Proteobacteria, Acidobacteria and Actinobacteria (dominant phylum for bacteria), and altitude had significant impacts on the Ascomycota, Basidiomycota and Mucoromycota (dominant phylum for fungi). The diversity of bacterial and fungal communities showed a monotonous decrease and increase with altitude. The influence of altitude on bacterial and fungal community composition was greater than that of soil depth. The variation of pH and dissolved organic nitrogen (DON) content in different altitudes were the main factors driving the bacterial and fungal community structure, respectively. There is no obvious difference between the network structure of surface and subsurface soil fungal communities, while the network of subsurface soil bacterial communities was more complex and compact than the surface layer. The network nodes mainly belonging to Proteobacteria and Actinobacteria are the key species in the two soil layers. Our results demonstrated that the altitude had a stronger influence on soil bacterial and fungal communities than soil depth, and bacterial and fungal communities showed divergent patterns along the altitudes and soil profiles.

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Comparative Analysis of Fungal Diversity in Rhizospheric Soil from Wild and Reintroduced Magnolia sinica Estimated via High-Throughput Sequencing

Plants ◽

10.3390/plants9050600 ◽

2020 ◽

Vol 9 (5) ◽

pp. 600

Author(s):

Qingqing Shen ◽

Junyu Yang ◽

Daifa Su ◽

Zhiying Li ◽

Wei Xiao ◽

...

Keyword(s):

Endangered Species ◽

Community Composition ◽

Fungal Community ◽

High Throughput Sequencing ◽

Fungal Communities ◽

Future Research ◽

Its2 Region ◽

Rhizospheric Soil ◽

Fungal Community Composition ◽

Opposite Pattern

Magnolia sinica is a critically endangered species and considered a “plant species with extremely small populations” (PSESP). It is an endemic species in southeastern Yunnan Province, China, with reproductive barriers. Rhizosphere fungi play a crucial role in plant growth and health. However, the composition, diversity, and function of fungal communities in wild and reintroduced M. sinica rhizospheres remain unknown. In this study, Illumina sequencing of the internal transcribed spacer 2 (ITS2) region was used to analyze rhizospheric soil samples from wild and reintroduced M. sinica. Thirteen phyla, 45 classes, 105 orders, 232 families, and 433 genera of fungi were detected. Basidiomycota and Ascomycota were dominant across all samples. The fungal community composition was similar between the wild and reintroduced rhizospheres, but the fungal taxa relative abundances differed. The fungal community richness was higher in the reintroduced rhizosphere than in the wild rhizosphere, but the diversity showed the opposite pattern. Soil nutrients and leaf litter significantly affected the fungal community composition and functional diversity. Here, the composition, structure, diversity, and ecological functions of the fungal communities in the rhizospheres of wild and reintroduced M. sinica were elucidated for the first time, laying a foundation for future research and endangered species protection.

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Metabarcoding of Soil Fungal Communities from Perturbed Areas Reveal Drive Role of Environmental Factors in Microbial Diversity of Colombian Andosols

10.21203/rs.3.rs-1128776/v1 ◽

2021 ◽

Author(s):

RAUL ALEXANDER ARANGUREN AROCA ◽

Samuele Voyron ◽

Fabrizio Ungaro ◽

Julio Cañón ◽

Erica Lumini

Keyword(s):

Land Use ◽

Fungal Community ◽

Mycorrhizal Fungi ◽

Alpha Diversity ◽

Arbuscular Mycorrhizal ◽

Conservation Agriculture ◽

Illumina Miseq ◽

Fungal Communities ◽

Its2 Region ◽

Fungal Community Composition

Abstract Changes in soil fungal community caused by land use have not been sufficiently studied in South-American Andosols, considered globally as important food production areas. This study analyzed 26 soil samples of Andosols collected from locations devoted to conservation, agriculture and mining activities in the southeastern region of Antioquia, Colombia, to establish differences between fungal communities as indicators of the degree of soil perturbation. The study developed a novel heminested PCR with primers SSUmCf Mix, ITS4 and fITS7 to assess Arbuscular Mycorrhizal Fungi detection in a Illumina MiSeq metabarcoding on nuclear ribosomal ITS2 region. A non-metric multidimensional scaling allowed exploring driver factors of fungal community changes, while fitted Dirichlet-multinomial models and PERMANOVA tests allowed identifying the correlations between alpha diversity indexes and community dissimilarities, as well as the significance of land use effects on fungal community composition. Furthermore, response ratios were determined to assess effect size by land use over relevant taxa. Results suggest a good coverage of fungal diversity with a detection of 10,529 high-quality ITS2 sequences belonged to phylum Glomeromycota. The analysis shows strong correlations of Shannon and Fisher indexes with dissimilarities on fungal communities among land uses (r=0.94), related to variations in temperature, air humidity and organic matter contents that lead to significant responses in abundances of relevant orders (such as Wallemiales and Trichosporonales). The study highlights the rich fungal biodiversity of the tropical Andosols, their specific sensitivities to environmental perturbation factors, and the useful range of a metabarcoding approach to characterize soil fungal communities.

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Diversity of rhizosphere and endophytic fungi in Atractylodes macrocephala during continuous cropping

PeerJ ◽

10.7717/peerj.8905 ◽

2020 ◽

Vol 8 ◽

pp. e8905

Author(s):

Bo Zhu ◽

Jianjun Wu ◽

Qingyong Ji ◽

Wei Wu ◽

Shihui Dong ◽

...

Keyword(s):

Endophytic Fungi ◽

Root Rot ◽

Negative Impact ◽

Illumina Miseq ◽

Fungal Communities ◽

Continuous Cropping ◽

Plant Fitness ◽

Fungal Community Composition ◽

Negative Effect ◽

Atractylodes Macrocephala

Rhizospheric and endophytic fungi are key factors which influence plant fitness and soil fertility. Atractylodes macrocephala is one of the best-known perennial herbs used in traditional Chinese medicine. Continuous cropping has been shown to have a negative effect on its growth and renders it more susceptible to microbial pathogen attacks. In this study, we investigated the effects of continuous cropping on the endophytic and rhizospheric fungi associated with A. macrocephala using culture-independent Illumina MiSeq. Continuous cropping was found to decrease fungal diversity inside plant roots, stems, leaves and tubers. Additionally, we found that the structure and diversity of rhizospheric and endophytic fungal communities were altered by root-rot disease. Fusarium was overrepresented among root-rot rhizospheric and endophytic fungi, indicating that it has a major negative impact on plant health during A. macrocephala monocropping. Canonical correspondence analysis of the control and diseased samples revealed that pH, hydrolysis N, electrical conductivity and Hg content were well-correlated with fungal community composition during continuous cropping. Taken together, these results highlight the ecological significance of fungal communities in maintaining plant fitness and will guide the development strategies to attenuate the negative impacts of A. macrocephala continuous cropping.

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Pollutant-Removing Biofilter Strains Associated with High Ammonia and Hydrogen Sulfide Removal Rate in a Livestock Wastewater Treatment Facility

Sustainability ◽

10.3390/su13137358 ◽

2021 ◽

Vol 13 (13) ◽

pp. 7358

Author(s):

Dong-Hyun Kim ◽

Hyun-Sik Yun ◽

Young-Saeng Kim ◽

Jong-Guk Kim

Keyword(s):

Wastewater Treatment ◽

Hydrogen Sulfide ◽

Microbial Community ◽

Microbial Communities ◽

Illumina Miseq ◽

Illumina Miseq Sequencing ◽

Miseq Sequencing ◽

Treatment Facility ◽

Livestock Wastewater ◽

Wastewater Treatment Facility

This study analyzed the microbial community metagenomically to determine the cause of the functionality of a livestock wastewater treatment facility that can effectively remove pollutants, such as ammonia and hydrogen sulfide. Illumina MiSeq sequencing was used in analyzing the composition and structure of the microbial community, and the 16S rRNA gene was used. Through Illumina MiSeq sequencing, information such as diversity indicators as well as the composition and structure of microbial communities present in the livestock wastewater treatment facility were obtained, and differences between microbial communities present in the investigated samples were compared. The number of reads, operational taxonomic units, and species richness were lower in influent sample (NLF), where the wastewater enters, than in effluent sample (NL), in which treated wastewater is found. This difference was greater in June 2019 than in January 2020, and the removal rates of ammonia (86.93%) and hydrogen sulfide (99.72%) were also higher in June 2019. In both areas, the community composition was similar in January 2020, whereas the influent sample (NLF) and effluent sample (NL) areas in June 2019 were dominated by Proteobacteria (76.23%) and Firmicutes (67.13%), respectively. Oleiphilaceae (40.89%) and Thioalkalibacteraceae (12.91%), which are related to ammonia and hydrogen sulfide removal, respectively, were identified in influent sample (NLF) in June 2019. They were more abundant in June 2019 than in January 2020. Therefore, the functionality of the livestock wastewater treatment facility was affected by characteristics, including the composition of the microbial community. Compared to Illumina MiSeq sequencing, fewer species were isolated and identified in both areas using culture-based methods, suggesting Illumina MiSeq sequencing as a powerful tool to determine the relevance of microbial communities for pollutant removal.

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Analysis of bacterial diversity of Chinese Luzhou-flavor liquor brewed in different seasons by Illumina Miseq sequencing

Annals of Microbiology ◽

10.1007/s13213-016-1223-5 ◽

2016 ◽

Vol 66 (3) ◽

pp. 1293-1301 ◽

Cited By ~ 25

Author(s):

Weining Sun ◽

Huazhi Xiao ◽

Qian Peng ◽

Qiaoge Zhang ◽

Xingxing Li ◽

...

Keyword(s):

Bacterial Diversity ◽

Illumina Miseq ◽

Illumina Miseq Sequencing ◽

Miseq Sequencing ◽

Different Seasons

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Do fungi and bacteria respond similar across a steep local pH gradient?

10.5194/egusphere-egu21-5720 ◽

2021 ◽

Author(s):

Rasmus Kjoller ◽

Carla Cruz-Paredes

Keyword(s):

Community Composition ◽

Soil Ph ◽

Wood Ash ◽

Ph Gradient ◽

Fungal Communities ◽

Ph Effects ◽

Fungal Community Composition ◽

Ph Gradients ◽

Field Samples ◽

Bacterial Richness

Soil pH is consistently recorded as the single most important variable explaining bacterial richness and community composition locally as globally. Bacterial richness responds to soil pH in a bell-shaped pattern, highest in soils with near-neutral pH, while lower diversity is found in soil with pH >8 and <4.5. Also, community turnover is strongly determined by pH for bacteria. In contrast, pH effects on fungi is apparently less pronounced though also much less studied compared to bacteria. Still, pH appears to be a significant determinant for fungal communities but typically not the most important. Rarely are bacterial and fungal communities co-analyzed from the same field samples taken across pH gradients. Here we analyze the community responses of fungi and bacteria in parallel over an extreme pH gradient ranging from pH 4 to 8 established by applying strongly alkaline wood ash to replicated plots in a Picea abies plantation. Bacterial and fungal community composition were assessed by amplicon-based meta-barcoding. Bacterial richness were not significantly affected by pH, while fungal richness and a-diversity were stimulated with higher pH. We found that both, bacterial and fungal communities increasingly deviated from the untreated plots with increasing amount of wood ash though fungal communities were more resistant to changes than bacterial. Soil NH4, NO3 and pH significantly correlated with the NMDS pattern for both bacterial and fungal communities. In the presentation we will discuss resistance versus sensitivity of different fungal functional guilds towards higher pH as well as the underlying factors explaining the community changes.

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Comparing dental plaque microbiome diversity of extrinsic black stain in the primary dentition using Illumina MiSeq sequencing technique

BMC Oral Health ◽

10.1186/s12903-019-0960-9 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Lulu Chen ◽

Qiong Zhang ◽

Yan Wang ◽

Keke Zhang ◽

Jing Zou

Keyword(s):

Relative Abundance ◽

Dental Plaque ◽

Illumina Miseq ◽

Primary Dentition ◽

Tooth Surface ◽

Oral Microbiota ◽

Illumina Miseq Sequencing ◽

Miseq Sequencing ◽

Cross Sectional ◽

Sequencing Technique

Abstract Background Extrinsic black stain (EBS) is characterized by discrete dark dots or lines on the tooth surface. The relationship between EBS and oral microbiota in children remains elusive. The aim of this study was to compare dental plaque microbiome in EBS children with that in EBS-free children in the primary dentition. Methods The Illumina MiSeq sequencing technique was utilized in the cross-sectional pilot study to investigate the diversity and composition of the supragingival plaque microbiota from 10 EBS-positive and 10 EBS-free children. The results were analysed with nonparametric Mann-Whitney U test, Pearson Chi-Square test, Fisher’s Exact test and one-way ANOVA tests. Results We identified 13 different phyla, 22 classes, 33 orders, 54 families, 105 genera, and 227 species from a total of 52,646 high-quality sequences. Between two groups, no statistical differences were observed in the estimators of community richness and diversity at 97% similarity, as well as in the Unweighted Unifrac principal co-ordinates analysis (PCoA). At the species level, higher level of relative abundance of Actinomyces naeslundii and lower level of relative abundance of a species belonging to Candidate_division_TM7 was observed in dental plaque of EBS-positive subjects, compared to dental plaque of EBS-free subjects (P < 0.05). This indicated that some species might be involved in the EBS process. Conclusion Changes in dental plaque microbiota is possibly relevant to the process of EBS in the primary dentition.

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