scholarly journals Influence of Tall Fescue Epichloë Endophytes on Rhizosphere Soil Microbiome

2021 ◽  
Vol 9 (9) ◽  
pp. 1843
Author(s):  
Kishan Mahmud ◽  
Kendall Lee ◽  
Nicholas S. Hill ◽  
Anaas Mergoum ◽  
Ali Missaoui
Keyword(s):  
Tall Fescue ◽  
Fungal Community ◽  
Fungal Endophytes ◽  
Plant Performance ◽  
Soil Microbiome ◽  
Available Phosphorus ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Endophyte Infection ◽  
Soil Bacterial

Tall fescue (Lolium arundinaceum (Schreb.) S.J. Darbyshire) often forms a symbiotic relationship with fungal endophytes (Epichloë coenophiala), which provides increased plant performance and greater tolerance to environmental stress compared to endophyte-free tall fescue. Whether this enhanced performance of tall fescue exclusively results from the grass–fungus symbiosis, or this symbiosis additionally results in the recruitment of soil microbes in the rhizosphere that in turn promote plant growth, remain a question. We investigated the soil bacterial and fungal community composition in iron-rich soil in the southeastern USA, and possible community shifts in soil microbial populations based on endophyte infection in tall fescue by analyzing the 16s rRNA gene and ITS specific region. Our data revealed that plant-available phosphorus (P) was significantly (p < 0.05) influenced by endophyte infection in tall fescue. While the prominent soil bacterial phyla were similar, a clear fungal community shift was observed between endophyte-infected (E+) and endophyte-free (E−) tall fescue soil at the phylum level. Moreover, compared to E− soil, E+ soil showed a greater fungal diversity at the genus level. Our results, thus, indicate a possible three-way interaction between tall fescue, fungal endophyte, and soil fungal communities resulting in improved tall fescue performance.

scholarly journals Influence of Tall Fescue Epichloë endophytes on Rhizosphere Soil Microbiome

2021 ◽  
Author(s):  
Kishan Mahmud ◽  
Kendall Lee ◽  
Nicholas Hill ◽  
Ali Missaoui
Keyword(s):  
Tall Fescue ◽  
Fungal Community ◽  
Soil Microbial Communities ◽  
The United States ◽  
Fungal Endophyte ◽  
Plant Performance ◽  
Soil Microbiome ◽  
Grass Species ◽  
Rrna Gene ◽  
Soil Microbial

Abstract Background Tall fescue (Lolium arundinaceum (Schreb.) S.J. Darbyshire) is a popular perennial grass species for livestock production and amenities in the United States. Tall fescue often forms a symbiotic relationship with fungal endophytes (Epichloë coenophiala) which provides increased plant tolerance to environmental stress compared to endophyte-free plants. However, whether this improved plant performance is the sole result of the unique relationship between the grass and the shoot-dwelling fungal endophyte of rhizosphere origin remains a question. This symbiosis possibly regulates the recruitment of beneficial soil microbial communities in endophyte-infected tall fescue rhizosphere and may offer enhanced nutrients and water acquisition, thereby, providing the plant with an increased tolerance level against environmental stresses. We compared the soil bacterial and fungal community composition and investigated possible community shifts in soil microbial populations based on endophyte infection in tall fescue by analyzing the 16s rRNA gene and ITS specific region. Results Our data revealed that bacterial community richness and the evenness indicated by Shannon Diversity Index (SDI) was greater than 4 in both endophyte-infected and endophyte-free tall fescue soil. In both types tall fescue soil, the prominent bacterial families were Planctomycetaceae, Balstocatellaceae_(subgroup_4), Chitinophagaceae, and Bacillaceae. In the case of soil fungal diversity, the SDI was overall low and ranged between 1.21 for endophyte-free and 1.27 for endophyte-infected tall fescue soil. The prominent fungal phyla were Basidiomycota and Ascomycota, and we observed a clear fungal community difference between endophyte-infected and endophyte-free soil at the phylum level. Moreover, endophyte-infected tall fescue soil showed a greater diversity at the genus level compared to endophyte-free tall fescue soil. In addition, plant-available soil phosphorus (P) is also influenced by the presence of endophytes in tall fescue. Conclusion Our results indicate that there is a tripartite relationship between tall fescue, the presence of fungal endophyte in the tall fescue, and the below-ground soil fungal communities. The dynamic of this three-way interaction perhaps contributes to the nutrient acquisition and stress tolerance by tall fescue possibly by recruiting a diverse array of potentially beneficial soil microbes.

scholarly journals Intraspecific variability in root traits and edaphic conditions influence soil microbiomes across 12 switchgrass cultivars

2020 ◽  
Author(s):  
Tayler Chicoine Ulbrich ◽  
Maren Friesen ◽  
Sarah S Roley ◽  
Lisa K Tiemann ◽  
Sarah E Evans
Keyword(s):  
Microbial Biomass ◽  
Fungal Community ◽  
Panicum Virgatum ◽  
Microbial Biomass Carbon ◽  
Intraspecific Variability ◽  
Root Traits ◽  
Soil Microbiome ◽  
Soil Conditions ◽  
Bacterial Phyla ◽  
Environmental Responses

Microbial communities help plants access nutrients and tolerate stress. Some microbiomes are specific to plant genotypes and, therefore, may contribute to intraspecific differences in plant growth and be a promising target for plant breeding. Switchgrass (Panicum virgatum L.) is a potential bioenergy crop with broad variation in yields and environmental responses; recent studies suggest that associations with distinct microbiomes may contribute to variation in cultivar yields. We used a common garden experiment to investigate variation in 12 mature switchgrass cultivar soil microbiomes and, further, to examine how root traits and soil conditions influence microbiome structure. We found that average root diameter varied up to 33% among cultivars and that they associated with distinct soil microbiomes. Cultivar had a larger effect on the soil bacterial than fungal community, but both were strongly influenced by soil properties. Root traits had a weaker effect on microbiome structure, but root length contributed to variation in the fungal community. Unlike the soil communities, the root bacterial communities did not group by cultivar, based on a subset of samples. Microbial biomass carbon and nitrogen and the abundance of several dominant bacterial phyla varied between ecotypes, but overall the differences in soil microbiomes were greater among cultivars than between ecotypes. Our findings show that there is not one soil microbiome that applies to all switchgrass cultivars, or even to each ecotype. These subtle but significant differences in root traits, microbial biomass, and the abundance of certain soil bacteria could explain differences in cultivar yields and environmental responses.

scholarly journals Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere

2008 ◽  
Vol 74 (17) ◽  
pp. 5422-5428 ◽  
Author(s):  
Mostafa S. Elshahed ◽  
Noha H. Youssef ◽  
Anne M. Spain ◽  
Cody Sheik ◽  
Fares Z. Najar ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Tall Grass ◽  
Data Set ◽  
Bacterial Phyla ◽  
Rare Biosphere ◽  
Soil Bacterial ◽  
Close Relatives ◽  
Taxonomic Groups

ABSTRACT Soil bacterial communities typically exhibit a distribution pattern in which most bacterial species are present in low abundance. Due to the relatively small size of most culture-independent sequencing surveys, a detailed phylogenetic analysis of rare members of the community is lacking. To gain access to the rarely sampled soil biosphere, we analyzed a data set of 13,001 near-full-length 16S rRNA gene clones derived from an undisturbed tall grass prairie soil in central Oklahoma. Rare members of the soil bacterial community (empirically defined at two different abundance cutoffs) represented 18.1 to 37.1% of the total number of clones in the data set and were, on average, less similar to their closest relatives in public databases when compared to more abundant members of the community. Detailed phylogenetic analyses indicated that members of the soil rare biosphere either belonged to novel bacterial lineages (members of five novel bacterial phyla identified in the data set, as well as members of multiple novel lineages within previously described phyla or candidate phyla), to lineages that are prevalent in other environments but rarely encountered in soil, or were close relatives to more abundant taxa in the data set. While a fraction of the rare community was closely related to more abundant taxonomic groups in the data set, a significant portion of the rare biosphere represented evolutionarily distinct lineages at various taxonomic cutoffs. We reason that these novelty and uniqueness patterns provide clues regarding the origins and potential ecological roles of members of the soil's rare biosphere.

scholarly journals Niche Selection by Soil Bacterial Community of Disturbed Subalpine Forests in Western Sichuan

Forests ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 505
Author(s):  
Zheliang Sheng ◽  
Wanze Zhu ◽  
Huaiying Yao ◽  
Shumiao Shu ◽  
Xia Li ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Secondary Forest ◽  
Soil Bacterial Community ◽  
Available Phosphorus ◽  
Rrna Gene ◽  
Western Sichuan ◽  
Local Soil ◽  
Soil Bacterial

Soil bacterial microbial communities are important in the ecosystem function and succession of forests. Using high-throughput 16S rRNA gene sequencing and relative importance for linear regression, we explored how the structures of soil bacterial community were influenced by the environmental factors and restoration succession of secondary forests in the Miyaluo Mountains of western Sichuan, China. Using a space-for-time approach, field measurements and sampling were conducted in four stands at different stages of natural restoration. Results of distance-based multivariate analysis showed that soil pH, organic carbon, available phosphorus, and C/N ratio were the predominant environmental factors that collectively explained a 46.9% variation in the bacterial community structures. The community compositions were jointly controlled by the direct and indirect effects of the rehabilitation stages. The changes in soil environmental factors coincided with restoration succession could lead to the shifts in the relative abundance of different soil bacterial taxa. We screened 13 successional discriminant taxa that could quantitatively indicate the secondary succession subalpine stage. Collectively, our findings show that soil bacteria in different taxa are governed by different local soil variables and rehabilitation ages, which can lead to shifts in the relative abundance of different taxa in successional stages, ultimately changing the entire soil bacterial community with the succession of secondary forest.

The driving factors of nematode gut microbiota under long-term fertilization

2020 ◽  
Vol 96 (4) ◽  
Author(s):  
Fei Zheng ◽  
Dong Zhu ◽  
Qing-Lin Chen ◽  
Qing-Fang Bi ◽  
Xiao-Ru Yang ◽  
...  
Keyword(s):  
Organic Matter ◽  
Gut Microbiota ◽  
Soil Properties ◽  
Gut Microbiome ◽  
Plant Litter ◽  
Driving Factors ◽  
Soil Microbiome ◽  
Available Phosphorus ◽  
Rrna Gene

ABSTRACT Animal bodies are colonized by many microorganisms which can provide indispensable services to their hosts. Although nematode gut microbiota has been extensively studied in recent years, the driving factors of gut microbiome of soil nematodes from a long-term fertilization field are unclear. Here, using 16S rRNA gene amplicon sequencing, we explored the nematode gut microbiota under different fertilization patterns (control, inorganic fertilizers and mixed fertilizers) and fertilization durations (5 y, 8 y and 10 y). Our results revealed that nematode gut microbiota was dominated by core bacterial taxa AF502208 (anaerobic bacteria), Enterobacter (plant litter decomposition) and Ancylobacter (organic matter decomposition and nitrogen cycling), significantly distinct from soil microbiome, and the assembly of that was a non-random process, which suggested host conditions contributed to maintaining the gut microbiota. Moreover, fertilization pattern had a greater influence on nematode gut microbiome than fertilization duration. Inorganic fertilization (5.19) significantly reduced the diversity of the nematode gut microbiota (6.68) shown by Shannon index (P &lt; 0.05). Canonical correspondence analysis demonstrates that soil properties such as pH, organic matter, total phosphorus, available phosphorus, ammonium nitrogen, moisture content, nitrate nitrogen and total nitrogen have significant effects on the nematode microbiome. Structured equation models further revealed that fertilization could obviously affect the nematode gut microbiota, and the effects were maintained even when accounting simultaneously for the drivers of soil bacteria and soil properties. This study provides a solid evidence that the shifting of nematode gut microbiota under long-term fertilization was resulted from environmental factors and host conditions, and advance the insights into host-microbiome in the agricultural ecosystems.

Agronomic advantages conferred by endophyte infection of perennial ryegrass (Lolium perenne L.) and tall fescue (Festuca arundinacea Schreb.) in Australia

2014 ◽  
Vol 65 (8) ◽  
pp. 747 ◽  
Author(s):  
D. E. Hume ◽  
J. C. Sewell
Keyword(s):  
Perennial Ryegrass ◽  
Tall Fescue ◽  
Festuca Arundinacea ◽  
Field Experiments ◽  
Insect Pests ◽  
Fungal Endophytes ◽  
High Stress ◽  
Agronomic Performance ◽  
Eastern Australia ◽  
Endophyte Infection

Perennial ryegrass and tall fescue are key grasses of sown pastures in the high-rainfall zone of south-eastern Australia. Ryegrass in naturalised pastures, and in sown seed, is widely infected with Neotyphodium fungal endophytes, with toxic endophyte strains occasionally causing toxicosis in livestock. Endophyte infection is also beneficial in sown grasslands, assisting ryegrass hosts to overcome biotic stresses, and tall fescue hosts to overcome biotic and abiotic stresses. We review the literature for Australia and present new data, to examine the agronomic effects of endophyte. Frequency of endophyte infection in old, perennial ryegrass pastures and ecotype-based cultivars is high and, in all pastures, increases with time, providing evidence for endophyte-infected plants having an agronomic advantage over endophyte-free plants. Within a cultivar, agronomic field experiments have compared endophyte-infected with endophyte-free swards. Endophyte significantly improved ryegrass establishment in seven of 19 measurements taken from 12 trials. In mature ryegrass pastures, over half of the experiments found advantages to endophyte infection. Tall fescues infected with a selected endophyte (‘AR542’) had improved agronomic performance relative to endophyte-free in a majority of experiments, and on occasions, the endophyte was essential for tall fescue persistence. Cultivar × endophyte interactions occurred but were inconsistent. In high-stress environments, endophyte was more important for agronomic performance than difference between cultivars. The relative importance of cultivar and endophyte is discussed, with elite cultivars that are adapted to the region and are infected with elite endophytes being the best avenue to capture the benefits and minimise detrimental endophyte effects on livestock. The major drivers are likely to be insect pests and drought, but evidence is limited.

scholarly journals Gut Microbiome in a Russian Cohort of Pre- and Post-Cholecystectomy Female Patients

2021 ◽  
Vol 11 (4) ◽  
pp. 294
Author(s):  
Irina Grigor’eva ◽  
Tatiana Romanova ◽  
Natalia Naumova ◽  
Tatiana Alikina ◽  
Alexey Kuznetsov ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
Gallstone Disease ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Female Patients ◽  
Composition And Structure ◽  
Before And After

The last decade saw extensive studies of the human gut microbiome and its relationship to specific diseases, including gallstone disease (GSD). The information about the gut microbiome in GSD-afflicted Russian patients is scarce, despite the increasing GSD incidence worldwide. Although the gut microbiota was described in some GSD cohorts, little is known regarding the gut microbiome before and after cholecystectomy (CCE). By using Illumina MiSeq sequencing of 16S rRNA gene amplicons, we inventoried the fecal bacteriobiome composition and structure in GSD-afflicted females, seeking to reveal associations with age, BMI and some blood biochemistry. Overall, 11 bacterial phyla were identified, containing 916 operational taxonomic units (OTUs). The fecal bacteriobiome was dominated by Firmicutes (66% relative abundance), followed by Bacteroidetes (19%), Actinobacteria (8%) and Proteobacteria (4%) phyla. Most (97%) of the OTUs were minor or rare species with ≤1% relative abundance. Prevotella and Enterocossus were linked to blood bilirubin. Some taxa had differential pre- and post-CCE abundance, despite the very short time (1–3 days) elapsed after CCE. The detailed description of the bacteriobiome in pre-CCE female patients suggests bacterial foci for further research to elucidate the gut microbiota and GSD relationship and has potentially important biological and medical implications regarding gut bacteria involvement in the increased GSD incidence rate in females.

scholarly journals An experimental intraradicular biofilm model in the pig for evaluating irrigation techniques

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Toshinori Tanaka ◽  
Yoshio Yahata ◽  
Keisuke Handa ◽  
Suresh V. Venkataiah ◽  
Mary M. Njuguna ◽  
...  
Keyword(s):  
16S Rrna ◽  
Root Canal ◽  
Apical Periodontitis ◽  
Exposure Model ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Bacterial Phyla ◽  
Biofilm Model ◽  
Biofilm Removal

Abstract Background We established an in vivo intraradicular biofilm model of apical periodontitis in pigs in which we compared the efficacy of different irrigant activation techniques for biofilm removal. Methods Twenty roots from the deciduous mandibular second premolar of 5 male pigs were used. After pulpectomy, canals were left open for 2 weeks and then sealed for 4 weeks to enable the development of an intracanal biofilm. The intraradicular biofilms was evaluated using SEM and bacterial 16S rRNA gene-sequencing. To investigate the efficacy of biofilm removal, root canal irrigations were performed using conventional needle, passive ultrasonic, subsonic, or laser-activated irrigation. Real-time PCR was conducted to quantitate the remaining biofilm components. Statistical analysis was performed using ANOVA followed by a Tukey kramer post-hoc test with α = 0.05. Results The pulp exposure model was effective in inducing apical periodontitis and SEM analysis revealed a multi-layer biofilm formation inside the root canal. 16S rRNA sequence analysis identified Firmicutes, Bacteroidetes, and Fusobacteria as the predominant bacterial phyla components, which is similar to the microbiome profile seen in humans. None of the tested irrigation techniques completely eradicated the biofilm components from the root canal, but the subsonic and laser-activated irrigation methods produced the lowest bacterial counts (p < 0.05). Conclusions An experimental intraradicular biofilm model has been successfully established in pigs. Within the limitations of the study, subsonic or laser-activated irrigation demonstrated the best biofilm removal results in the pig system.

Sign in / Sign up

Export Citation Format

Share Document