scholarly journals Taxonomic and Functional Composition of Soil Mycobiome of Two Agricultural Sites in Khartoum State, Sudan

2021 ◽  
Author(s):  
Marwa H. E. Elnaiem ◽  
Takeshi Taniguchi ◽  
Marmar El Siddig
Keyword(s):  
Land Use ◽  
Community Structure ◽  
Fungal Community ◽  
Alpha Diversity ◽  
Shannon Index ◽  
Fungal Community Composition ◽  
Fungal Community Structure ◽  
Land Use Types ◽  
Diverse Groups ◽  
First Time

Abstract Fungi are one of the most diverse groups of organisms and considered as one of the least-explored biodiversity resources. Soil fungal community was investigated in two agricultural sites in Khartoum state, Sudan, during two seasons. A total of 42 soil samples were collected, their physicochemical properties were determined, then subjected to metabarcoding and metagenomic analyses. fungal community composition, diversity and microbial trophic modes were determined utilizing R software packages. From both sites, a total of 15 different phyla were detected, out of them, 11 were the most abundant and frequent. Ascomycota was the dominant phylum (86.54% total abundance), followed by the Basidiomycota (8.29%). The dominant class was Sordariomycetes (41.02%), followed by Dothideomycetes (19.80%). Aspergillus (6.2%), Curvularia (6.0%), Neurospora (5.8%) and Fusarium (4.9%) were the most abundant genera. Deniquelata for the first time being recorded in Sudan. Apha diversity measures revealed sample richness ranging from 71 to 361 ASVs, and Shannon index ranging from 2.794 to 5.087. The two sites had significantly different alpha diversity. Land-use types were also significantly different in their diversity regardless of site. Season had no effect on alpha diversity of soil fungal communities. Beta diversity analysis indicated significant differences between the two sites and the different land-use types. No significant differences in the community structure recorded between the two seasons. The dominant trophic mode among the assigned ASVs in soil mycobiome was saprotroph mode (22.11%). Results of this study reveals that fungal community structure is affected by site and land-use type. It gives a comprehensive database for the mycobiome of the agricultural soil in Khartoum state.

scholarly journals Dynamics of soil properties and fungal community structure in continuous-cropped alfalfa fields in Northeast China

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7127 ◽  
Author(s):  
Qin Yao ◽  
Yanxia Xu ◽  
Xuefeng Liu ◽  
Junjie Liu ◽  
Xinyu Huang ◽  
...  
Keyword(s):  
Community Structure ◽  
Soil Properties ◽  
Fungal Community ◽  
Continuous Cropping ◽  
Fungal Community Composition ◽  
Fungal Community Structure ◽  
P Content ◽  
Soil Fungal Community ◽  
Relative Abundances ◽  
Total P

To compensate for the seasonal imbalance between livestock and forage yield in the cold region of Northeast China, alfalfa (Medicago sativa L.) continuous cropping has been widely employed in animal husbandry. However, the effects of continuous cropping of alfalfa on soil properties, including physical, chemical and biological properties, are poorly understood. In this study, we investigated the soil properties and fungal community composition of alfalfa fields under continuous cropping for different time periods (i.e., 1, 2, 6, 9, 12, 13 and 35 years). The results showed that soil moisture, total C, total N, NO3−-N and available K content decreased at less than 10 years of continuous cropping and then increased at more than 10 years of continuous cropping, but soil total P and available P content showed the opposite tendency. The soil fungal community composition determined using Illumina Miseq sequencing showed that continuous cropping increased the fungal alpha diversity and changed the fungal community structure. The relative abundances of Guehomyces and Chaetomium decreased, but the relative abundances of Phaeomycocentrospora and Paecilomyces increased with continuous cropping time. In addition, continuous cropping of alfalfa increased the relative abundances of some plant pathogens, such as Haematonectria haematococca and Cyphellophora sp. Soil total P and available P content were important soil factors affecting the soil fungal community diversity, fungal community structure and the relative abundances of specific fungi in this alfalfa continuous cropping system.

scholarly journals Reassembly of soil fungal communities under reforestation and herbivore exclusion

2020 ◽  
Author(s):  
Shinichi Tatsumi ◽  
Shunsuke Matsuoka ◽  
Saori Fujii ◽  
Kobayashi Makoto ◽  
Takashi Osono ◽  
...  
Keyword(s):  
Community Structure ◽  
Fungal Community ◽  
Tree Species ◽  
Alpha Diversity ◽  
Ecosystem Restoration ◽  
Detectable Effect ◽  
Natural Forests ◽  
Degraded Land ◽  
Fungal Community Structure ◽  
Herbivore Exclusion

AbstractSoil fungi can help improve ecosystem restoration, yet our understanding of how fungi reassemble in degraded land is limited. Here, we studied fungal community structure using DNA metabarcoding in reforested sites following agricultural abandonment and overgrazing. We used a natural experiment in which reforestation with different numbers of tree species and deer exclusion have been applied for multiple decades. We found that local fungal richness (alpha diversity) was 1.9 to 2.9 times greater in reforested stands than in natural forests and total fungal richness (gamma diversity) was 1.3 to 1.9 times greater. These results were regardless of the number of tree species planted in the reforested stands. Conversely, reforested stands had a homogenized community structure with relatively lower degrees of compositional dissimilarity among sites within each stand (beta diversity). These findings were attributable to lower environmental heterogeneity, stronger dispersal limitation, and a comparatively shorter time since the onset of community assembly in reforested stands. Deer exclosures had no detectable effect on fungal community structure. Overall, the agricultural legacy in fungal community structure appears to have persisted for decades, even under proactive restoration of aboveground vegetation. Direct human intervention belowground may therefore be necessary for the recovery of soil biota once homogenized, which may facilitate ecosystem restoration.

scholarly journals Diversity of Endophytic Fungal Community in Leaves of Artemisia argyi Based on High-throughput Amplicon Sequencing

2021 ◽  
Vol 70 (2) ◽  
pp. 273-281
Author(s):  
QIU-FANG WU ◽  
LING-MIN HE ◽  
XIN-QIANG GAO ◽  
MEI-LING ZHANG ◽  
JING-SHUN WANG ◽  
...  
Keyword(s):  
Community Structure ◽  
High Throughput ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Fungal Community Structure ◽  
Operational Taxonomic Units ◽  
Artemisia Argyi ◽  
Artemisia Species

To investigate the community structure and diversity of endophytic fungi in the leaves of Artemisia argyi, leaf samples were collected from five A. argyi varieties grown in different cultivation areas in China, namely, Tangyin Beiai in Henan (BA), Qichun Qiai in Hubei (QA), Wanai in Nanyang in Henan (WA), Haiai in Ningbo in Zhejiang (HA), and Anguo Qiai in Anguo in Hebei (AQA), and analyzed using Illumina high-throughput sequencing technology. A total of 365,919 pairs of reads were obtained, and the number of operational taxonomic units for each sample was between 165 and 285. The alpha diversity of the QA and BA samples was higher, and a total of two phyla, eight classes, 12 orders, 15 families, and 16 genera were detected. At the genus level, significant differences were noted in the dominant genera among the samples, with three genera being shared in all the samples. The dominant genus in QA was Erythrobasidium, while that in AQA, HA, and BA was Sporobolomyces, and that in WA was Alternaria, reaching a proportion of 16.50%. These results showed that the fungal community structure and diversity in QA and BA were high. The endophytes are of great importance to the plants, especially for protection, phytohormone and other phytochemical production, and nutrition. Therefore, this study may be significant with the industrial perspective of Artemisia species.

scholarly journals Diversity and community structure of Odonata (Insecta) in two land use types in Purba Medinipur District, West Bengal, India

2019 ◽  
Vol 11 (6) ◽  
pp. 13748-13755
Author(s):  
Priti Ranjan Pahari ◽  
Shubha Sankar Mandal ◽  
Subhadeep Maiti ◽  
Tanmay Bhattacharya
Keyword(s):  
Land Use ◽  
Industrial Pollution ◽  
Dominant Species ◽  
West Bengal ◽  
Shannon Index ◽  
Dominance Index ◽  
Faunal Composition ◽  
Land Use Types ◽  
First Time ◽  
Pantala Flavescens

The present study recorded a total of 45 species of Odonata, of which one species, Ischnura mildredae, was recorded for the first time from West Bengal in India.  Thirty-eight species were found in Tamluk Municipality as compared to 21 species in Haldia Industrial Belt (IB), with 14 species common to both the localities.  Index of similarity revealed that the two localities were slightly dissimilar in odonate faunal composition as only 47% of species were shared.  In both the localities, Anisoptera was more abundant, comprising over 69% of the total odonates.  Libellulidae was the most abundant Anisopteran family in both the localities, comprising over 66% of the total odonates.  Coenagrionidae was the most abundant Zygopteran family in both the localities.  Thirteen species of Anisoptera and 11 species of Zygoptera were found only in Tamluk whereas two species of Anisoptera and five species of Zygoptera were found only in Haldia IB.  Crocothemis servilia, Pantala flavescens, and Ceriagrion coromandelianum were the dominant species in Tamluk while Brachythemis contaminata and Orthetrum sabina were the dominant species in Haldia IB.  Based on the values of Shannon index, Tamluk was considered unpolluted (=3.16) and Haldia IB moderately polluted (=2.43).  Higher equitability index (J=0.87) and very low dominance index (0.06) in Tamluk indicated homogeneity in community composition and relatively stress-free equitable environment.  The present investigation suggests that Odonata can be used as bioindicators of industrial pollution.

scholarly journals Knowing your neighbourhood—the effects of Epichloë endophytes on foliar fungal assemblages in perennial ryegrass in dependence of season and land-use intensity

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4660 ◽  
Author(s):  
Julia König ◽  
Marco Alexandre Guerreiro ◽  
Derek Peršoh ◽  
Dominik Begerow ◽  
Jochen Krauss
Keyword(s):  
Land Use ◽  
Community Structure ◽  
Fungal Community ◽  
Grass Species ◽  
Rrna Gene ◽  
Land Use Intensity ◽  
Study Region ◽  
Fungal Community Structure ◽  
Fungal Assemblages ◽  
Study Sites

Epichloë endophytes associated with cool-season grass species can protect their hosts from herbivory and can suppress mycorrhizal colonization of the hosts’ roots. However, little is known about whether or not Epichloë endophyte infection can also change the foliar fungal assemblages of the host. We tested 52 grassland study sites along a land-use intensity gradient in three study regions over two seasons (spring vs. summer) to determine whether Epichloë infection of the host grass Lolium perenne changes the fungal community structure in leaves. Foliar fungal communities were assessed by Next Generation Sequencing of the ITS rRNA gene region. Fungal community structure was strongly affected by study region and season in our study, while land-use intensity and infection with Epichloë endophytes had no significant effects. We conclude that effects on non-systemic endophytes resulting from land use practices and Epichloë infection reported in other studies were masked by local and seasonal variability in this study’s grassland sites.

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

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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