A DGGE-cloning method to characterize arbuscular mycorrhizal community structure in soil

Liang, Zhanbei; Drijber, Rhae A.; Lee, Donald J.; Dwiekat, I.; Harris, Steven D.; Wedin, David A.

doi:10.1016/j.soilbio.2007.11.016

Cited by 83 publications

(57 citation statements)

References 54 publications

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“…This recalled the drawbacks of recovering sequence data from excised bands (Liang et al 2008). To obtain relatively longer sequences with higher phylogenetic resolution and more phylotypes of root-associated AMF, clone libraries were constructed using the primer pair AML1/AML2 which proved to be highly AMF-specific and allowed the amplification of a small subunit (SSU) rDNA fragment of ∼790 bp .…”

Section: Dna Extraction and Pcr Amplificationmentioning

confidence: 99%

Differential effects of abiotic factors and host plant traits on diversity and community composition of root-colonizing arbuscular mycorrhizal fungi in a salt-stressed ecosystem

Guo

Gong

2013

Mycorrhiza

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Arbuscular mycorrhizal fungi (AMF) were investigated in roots of 18 host plant species in a salinized south coastal plain of Laizhou Bay, China. From 18 clone libraries of 18S rRNA genes, all of the 22 AMF phylotypes were identified into Glomus, of which 18 and 4 were classified in group A and B in the phylogenetic tree, respectively. The phylotypes related to morphologically defined Glomus species occurred generally in soil with higher salinity. AMF phylotype richness, Shannon index, and evenness were not significantly different between root samples from halophytes vs. non-halophytes, invades vs. natives, or annuals vs. perennials. However, AMF diversity estimates frequently differed along the saline gradient or among locations, but not among pH gradients. Moreover, UniFrac tests showed that both plant traits (salt tolerance, life style or origin) and abiotic factors (salinity, pH, or location) significantly affected the community composition of AMF colonizers. Redundancy and variation partitioning analyses revealed that soil salinity and pH, which respectively explained 6.9 and 4.2 % of the variation, were the most influential abiotic variables in shaping the AMF community structure. The presented data indicate that salt tolerance, life style, and origin traits of host species may not significantly affect the AMF diversity in roots, but do influence the community composition in this salinized ecosystem. The findings also highlight the importance of soil salinity and pH in driving the distribution of AMF in plant and soil systems.

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Section: Dna Extraction and Pcr Amplificationmentioning

confidence: 99%

Differential effects of abiotic factors and host plant traits on diversity and community composition of root-colonizing arbuscular mycorrhizal fungi in a salt-stressed ecosystem

Guo

Gong

2013

Mycorrhiza

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“…Primarily, this technique is carried out by amplifying specific sequences of interest, such as ribosomal RNA (rRNA) genes (Cahyani et al, 2004;Zhao et al, 2012;Yan et al, 2013;Yoshitake et al, 2013). It is a quicker and less labor-intensive approach than sequencing clone libraries for comparing community composition across samples (Oros-Sichler et al, 2006;Liang et al, 2008). Besides, PCR-DGGE enables the detection of unculturable microorganisms and is better suited to the investigation of soil microbial diversity (Liang et al, 2008;Yan et al, 2013;Yoshitake et al, 2013;Najnin et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

“…It is a quicker and less labor-intensive approach than sequencing clone libraries for comparing community composition across samples (Oros-Sichler et al, 2006;Liang et al, 2008). Besides, PCR-DGGE enables the detection of unculturable microorganisms and is better suited to the investigation of soil microbial diversity (Liang et al, 2008;Yan et al, 2013;Yoshitake et al, 2013;Najnin et al, 2015). Therefore, it also formed an important part of this study.…”

Section: Introductionmentioning

confidence: 99%

Effect of karst rocky desertification on soil fungal communities in Southwest China

Wang¹,

Bt²,

Chen³

et al. 2016

Genet. Mol. Res.

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ABSTRACT. Karst mountainous ecosystems are associated with karst rocky desertification (KRD), which can greatly impact soil structure and function. Despite the importance of soil microbes as a major factor maintaining ecosystem stability, we know little about the effect on soil fungal communities of KRD in karst regions. We investigated this relationship across a gradient of KRD soils from Guizhou, China by polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE). Fungal diversity indices (Shannon-Wiener, richness, and evenness) significantly differed (P < 0.05) based on KRD severity, being lowest in moderately affected areas. Cluster analysis showed that the five sites examined clustered into two main groups according to KRD grade (high and low). Moreover, a homology search using sequences recovered from PCR-DGGE bands showed that the dominant fungi in each community varied remarkably, and included Aspergillus, Aphanoascus, Blastomyces, Fusarium, Glomus, Geomyces, Gibberella, Mortierella, Tetracladium, and Tumularia species, and an unclassified group. In conclusion, these findings demonstrate that KRD has a significant impact on soil fungal communities.

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“…In addition, these techniques make it possible to characterize and provide an in-depth description of the structure and succession of microorganisms in the soil (Novais et al, 2010). One of the common molecular techniques, PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis), is currently used to evaluate the profile of AMF communities from agricultural soils (Gollotte et al, 2004;Liang et al, 2008).…”

mentioning

confidence: 99%

Occurrence and Structure of Arbuscular Mycorrhizal Fungal Communities in Cassava after Cultivation of Cover Crops as Observed by the “PCR-DGGE” Technique

Heberle

Armas

Heberle

et al. 2015

Rev. Bras. Ciênc. Solo

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cassava (Manihot esculenta crantz) is a highly mycotrophic crop, and prior soil cover may affect the density of arbuscular mycorrhizal fungi (aMfs), as well as the composition of the aMfs community in the soil. the aim of this study was to evaluate the occurrence and the structure of aMfs communities in cassava grown after different cover crops, and the effect of the cover crop on mineral nutrition and cassava yield under an organic farming system. the occurrence and structure of the aMfs community was evaluated through polymerase chain reaction (pcr) and denaturing gradient gel electrophoresis (dgge). a randomized block

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A DGGE-cloning method to characterize arbuscular mycorrhizal community structure in soil

Abstract: Lee, Donald J.; Dwiekat, Ismail M.; Harris, Steven D.; and Wedin, David A., "A DGGE-cloning method to characterize arbuscular mycorrhizal community structure in soil" (2008). Papers in Plant Pathology. 95.

Cited by 83 publications

References 54 publications

Differential effects of abiotic factors and host plant traits on diversity and community composition of root-colonizing arbuscular mycorrhizal fungi in a salt-stressed ecosystem

Differential effects of abiotic factors and host plant traits on diversity and community composition of root-colonizing arbuscular mycorrhizal fungi in a salt-stressed ecosystem

Effect of karst rocky desertification on soil fungal communities in Southwest China

Occurrence and Structure of Arbuscular Mycorrhizal Fungal Communities in Cassava after Cultivation of Cover Crops as Observed by the “PCR-DGGE” Technique

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