scholarly journals Inoculation with Rhizophagus irregularis Does Not Alter Arbuscular Mycorrhizal Fungal Community Structure within the Roots of Corn, Wheat, and Soybean Crops

2020 ◽  
Vol 8 (1) ◽  
pp. 83 ◽  
Author(s):  
Sébastien Renaut ◽  
Rachid Daoud ◽  
Jacynthe Masse ◽  
Agathe Vialle ◽  
Mohamed Hijri
Keyword(s):  
Community Composition ◽  
Arbuscular Mycorrhizal ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Soil Samples ◽  
Rhizophagus Irregularis ◽  
Community Diversity ◽  
Reference Sequence ◽  
Growth Stages ◽  
Arbuscular Mycorrhizal Fungal

Little is known about establishment success of the arbuscular mycorrhizal fungal (AMF) inocula and their effects on a soil-indigenous community of AMF. In this study, we assessed the effect of introducing Rhizophagus irregularis DAOM-197198 in soil under field condition on the community composition of indigenous AMF in the roots of corn (Zea mays), soybean (Glycine max), and wheat (Triticum aestivum). Three field trials were conducted with inoculated and non-inoculated plots. Four to ten roots and their rhizosphere soil samples of two growth stages for corn and wheat, and one growing stage of soybean, were collected, totalling 122 root and soil samples. Root colonization was measured microscopically, and the fungal communities were determined by paired-end Illumina MiSeq amplicon sequencing using 18S rDNA marker. After quality trimming and merging of paired ends, 6.7 million sequences could be assigned to 414 different operational taxonomic units. These could be assigned to 68 virtual taxa (VT) using the AMF reference sequence database MaarjAM. The most abundant VT corresponded to R. irregularis. The inoculation treatment did not influence the presence of R. irregularis, or AMF community diversity in roots. This seems to indicate that inoculation with R. irregularis DAOM-197198 does not change the indigenous AMF community composition, probably because it is already present in high abundance naturally.

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

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.

scholarly journals Identifying Hidden Viable Bacterial Taxa in Tropical Forest Soils Using Amplicon Sequencing of Enrichment Cultures

Biology ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 569
Author(s):  
Chakriya Sansupa ◽  
Sara Fareed Mohamed Wahdan ◽  
Terd Disayathanoowat ◽  
Witoon Purahong
Keyword(s):  
Bacterial Community ◽  
Forest Soil ◽  
Culture Media ◽  
Enrichment Culture ◽  
Sequence Similarity ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Soil Samples ◽  
Enrichment Cultures ◽  
Total Community

This study aims to estimate the proportion and diversity of soil bacteria derived from eDNA-based and culture-based methods. Specifically, we used Illumina Miseq to sequence and characterize the bacterial communities from (i) DNA extracted directly from forest soil and (ii) DNA extracted from a mixture of bacterial colonies obtained by enrichment cultures on agar plates of the same forest soil samples. The amplicon sequencing of enrichment cultures allowed us to rapidly screen a culturable community in an environmental sample. In comparison with an eDNA community (based on a 97% sequence similarity threshold), the fact that enrichment cultures could capture both rare and abundant bacterial taxa in forest soil samples was demonstrated. Enrichment culture and eDNA communities shared 2% of OTUs detected in total community, whereas 88% of enrichment cultures community (15% of total community) could not be detected by eDNA. The enrichment culture-based methods observed 17% of the bacteria in total community. FAPROTAX functional prediction showed that the rare and unique taxa, which were detected with the enrichment cultures, have potential to perform important functions in soil systems. We suggest that enrichment culture-based amplicon sequencing could be a beneficial approach to evaluate a cultured bacterial community. Combining this approach together with the eDNA method could provide more comprehensive information of a bacterial community. We expected that more unique cultured taxa could be detected if further studies used both selective and non-selective culture media to enrich bacteria at the first step.

scholarly journals Arbuscular Mycorrhizal Fungal Communities in the Soils of Desert Habitats

2021 ◽  
Vol 9 (2) ◽  
pp. 229
Author(s):  
Martti Vasar ◽  
John Davison ◽  
Siim-Kaarel Sepp ◽  
Maarja Öpik ◽  
Mari Moora ◽  
...  
Keyword(s):  
Plant Root ◽  
Significant Proportion ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
Illumina Miseq ◽  
Desert Ecosystems ◽  
Fungal Dna ◽  
Root Symbionts ◽  
Arbuscular Mycorrhizal Fungal

Deserts cover a significant proportion of the Earth’s surface and continue to expand as a consequence of climate change. Mutualistic arbuscular mycorrhizal (AM) fungi are functionally important plant root symbionts, and may be particularly important in drought stressed systems such as deserts. Here we provide a first molecular characterization of the AM fungi occurring in several desert ecosystems worldwide. We sequenced AM fungal DNA from soil samples collected from deserts in six different regions of the globe using the primer pair WANDA-AML2 with Illumina MiSeq. We recorded altogether 50 AM fungal phylotypes. Glomeraceae was the most common family, while Claroideoglomeraceae, Diversisporaceae and Acaulosporaceae were represented with lower frequency and abundance. The most diverse site, with 35 virtual taxa (VT), was in the Israeli Negev desert. Sites representing harsh conditions yielded relatively few reads and low richness estimates, for example, a Saudi Arabian desert site where only three Diversispora VT were recorded. The AM fungal taxa recorded in the desert soils are mostly geographically and ecologically widespread. However, in four sites out of six, communities comprised more desert-affiliated taxa (according to the MaarjAM database) than expected at random. AM fungal VT present in samples were phylogenetically clustered compared with the global taxon pool, suggesting that nonrandom assembly processes, notably habitat filtering, may have shaped desert fungal assemblages.

scholarly journals Studies on the arbuscular mycorrhizal fungal association in some medicinal plant species of paithal hills, western ghats kannur district, kerala

2020 ◽  
Vol 7 (2) ◽  
pp. 30-38
Author(s):  
Santhoshkumar S ◽  
Nagarajan N ◽  
Sree Priya S
Keyword(s):  
Plant Species ◽  
Root Colonization ◽  
Rhizosphere Soil ◽  
Fungal Spores ◽  
Arbuscular Mycorrhizal ◽  
Soil Samples ◽  
Fungal Colonization ◽  
The Family ◽  
Spore Population ◽  
Arbuscular Mycorrhizal Fungal

In the present study to analyzed that the arbuscular mycorrhizal fungal spores in root colonization and spore population in rhizosphere soils samples in various medicinal at Paithal hills,Western Ghats of Kannur district, Kerala, India. Root and rhizosphere soil samples were collected during the month of August, 2018-March, 2019 from the surface to 30 cm depth as well as pH were also recorded. Totally 30 plant species belonging to 19 families were collected and identified. The present result showed arbuscular mycorrhizal spore population in the rhizosphere soil and root colonization of all the plant species. A total of 19 AM fungal spores were recovered from the rhizosphere soil samples in this study region. The Glomus was dominant had seen in rhizosphere soil samples in all the medicinal plant species. The maximum spore population was found in the rhizosphere soil samples of Mimosa pudica (590/100g of soil) which belongs to the family Mimosaceae and the lowest spore population was observed in the Terminalia bellirica 135/100g of soil) belongs to Combretaceae family. The highest  78 % AM fungal colonization was found in roots of Euphorbia hirta belongs to the family Euphorbiaceae. While the lowest 11 % AM fungal colonization was found in the root of Sida acuta belongs to the family Malvaceae.

Root colonization and arbuscular mycorrhizal fungal community composition in a genetically modified maize, its non-modified isoline, and a landrace

Mycorrhiza ◽  
2020 ◽  
Vol 30 (5) ◽  
pp. 611-621
Author(s):  
Diana Marcela Morales Londoño ◽  
Edenilson Meyer ◽  
Kelly Justin da Silva ◽  
Anabel González Hernández ◽  
Rafael Dutra de Armas ◽  
...  
Keyword(s):  
Community Composition ◽  
Fungal Community ◽  
Root Colonization ◽  
Genetically Modified ◽  
Arbuscular Mycorrhizal ◽  
Genetically Modified Maize ◽  
Fungal Community Composition ◽  
Arbuscular Mycorrhizal Fungal

Arbuscular mycorrhizal fungal community composition associated with Juniperus brevifolia in native Azorean forest

2017 ◽  
Vol 79 ◽  
pp. 48-61 ◽  
Author(s):  
Catarina Drumonde Melo ◽  
Sara Luna ◽  
Claudia Krüger ◽  
Christopher Walker ◽  
Duarte Mendonça ◽  
...  
Keyword(s):  
Community Composition ◽  
Fungal Community ◽  
Arbuscular Mycorrhizal ◽  
Fungal Community Composition ◽  
Arbuscular Mycorrhizal Fungal

scholarly journals Rapid response of arbuscular mycorrhizal fungal communities to short-term fertilization in an alpine grassland on the Qinghai-Tibet Plateau

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2226 ◽  
Author(s):  
Xingjia Xiang ◽  
Sean M. Gibbons ◽  
Jin-Sheng He ◽  
Chao Wang ◽  
Dan He ◽  
...  
Keyword(s):  
Arbuscular Mycorrhizal ◽  
Illumina Miseq ◽  
Tibet Plateau ◽  
Available Phosphorus ◽  
Short Term ◽  
Amf Diversity ◽  
Amf Communities ◽  
Arbuscular Mycorrhizal Fungal ◽  
The Impact ◽  
Qinghai Tibet Plateau

Background:The Qinghai-Tibet Plateau (QTP) is home to the vast grassland in China. The QTP grassland ecosystem has been seriously degraded by human land use practices and climate change. Fertilization is used in this region to increase vegetation yields for grazers. The impact of long-term fertilization on plant and microbial communities has been studied extensively. However, the influence of short-term fertilization on arbuscular mycorrhizal fungal (AMF) communities in the QTP is largely unknown, despite their important functional role in grassland ecosystems.Methods:We investigated AMF community responses to three years of N and/or P addition at an experimental field site on the QTP, using the Illumina MiSeq platform (PE 300).Results:Fertilization resulted in a dramatic shift in AMF community composition and NP addition significantly increased AMF species richness and phylogenetic diversity. Aboveground biomass, available phosphorus, and NO3−were significantly correlated with changes in AMF community structure. Changes in these factors were driven by fertilization treatments. Thus, fertilization had a large impact on AMF communities, mediated by changes in aboveground productivity and soil chemistry.Discussion:Prior work has shown how plants often lower their reliance on AMF symbioses following fertilization, leading to decrease AMF abundance and diversity. However, our study reports a rise in AMF diversity with fertilization treatment. Because AMF can provide stress tolerance to their hosts, we suggest that extreme weather on the QTP may help drive a positive relationship between fertilizer amendment and AMF diversity.

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