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

被引：72

作者：

Liang, Zhanbei ^{[1
]}

Drijber, Rhae A. ^{[1
]}

Lee, Donald J. ^{[1
]}

Dwiekat, Ismail M. ^{[1
]}

Harris, Steven D. ^{[2
]}

Wedin, David A. ^{[3
]}

机构：

[1] Univ Nebraska, Dept Agron & Hort, Lincoln, NE 68583 USA

[2] Univ Nebraska, Dept Plant Pathol, Lincoln, NE 68583 USA

[3] Univ Nebraska, Sch Nat Resources, Lincoln, NE 68583 USA

来源：

SOIL BIOLOGY & BIOCHEMISTRY | 2008年 / 40卷 / 04期

关键词：

18S rDNA; nested PCR; DGGE; clone; AMF community structure;

D O I：

10.1016/j.soilbio.2007.11.016

中图分类号：

S15 [土壤学];

学科分类号：

0903 ; 090301 ;

摘要：

Although arbuscular mycorrhizal fungi (AMF) are crucial for ecosystem functioning, characterizing AMF community structure in soil is challenging. In this study, nested polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) were combined with cloning of fungal 18S ribosomal gene fragments for the rapid comparison of AM F community structure in soil. Reference AMF isolates, representing four major genera of AMF, were used to develop the method. Sequential amplification of 18S rDNA fragments by nested PCR using primer pairs AMI-NS31 and Glo1-NS31GC followed by DGGE analysis yielded a high-resolution band profile. In parallel, 18S rDNA fragment clone libraries were constructed and clones screened by DGGE. Sequence identity was inferred by matching the electrophoretic mobility of the sample fingerprint bands to that of bands from individual clones. The effectiveness of this approach was tested on soil samples from different ecosystems, yielding reproducible, complex DGGE band patterns specific to each site. The coupling of PCR-DGGE with clone library analysis provides a robust, reliable, and precise means to characterize AM F community structure in soils. (C) 2007 Elsevier Ltd. All rights reserved.

引用

页码：956 / 966

页数：11

共 54 条

[31] PROFILING OF COMPLEX MICROBIAL-POPULATIONS BY DENATURING GRADIENT GEL-ELECTROPHORESIS ANALYSIS OF POLYMERASE CHAIN REACTION-AMPLIFIED GENES-CODING FOR 16S RIBOSOMAL-RNA [J].

MUYZER, G ;

DEWAAL, EC ;

UITTERLINDEN, AG .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 1993, 59 (03) :695-700

[32] Impact of land use intensity on the species diversity of arbuscular mycorrhizal fungi in agroecosystems of Central Europe [J].

Oehl, F ;

Sieverding, E ;

Ineichen, K ;

Mäder, P ;

Boller, T ;

Wiemken, A .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2003, 69 (05) :2816-2824

[33] Divergent arbuscular mycorrhizal fungal communities colonize roots of Pulsatilla spp. in boreal Scots pine forest and grassland soils [J].

Öpik, M ;

Moora, M ;

Liira, J ;

Koljalg, U ;

Zobel, M ;

Sen, R .

NEW PHYTOLOGIST, 2003, 160 (03) :581-593

[34] Organization of genetic variation in individuals of arbuscular mycorrhizal fungi [J].

Pawlowska, TE ;

Taylor, JW .

NATURE, 2004, 427 (6976) :733-737

[35] Rapid PCR-based method for the direct analysis of fungal communities in complex environmental samples [J].

Pennanen, T ;

Paavolainen, L ;

Hantula, J .

SOIL BIOLOGY & BIOCHEMISTRY, 2001, 33 (4-5) :697-699

[36] High levels of variation in ribosomal DNA sequences within and among spores of a natural population of the arbuscular mycorrhizal fungus Acaulospora colossica [J].

Pringle, A ;

Moncalvo, JM ;

Vilgalys, R .

MYCOLOGIA, 2000, 92 (02) :259-268

[37] Artisanal and experimental Pecorino Siciliano cheese: Microbial dynamics during manufacture assessed by culturing and PCR-DGGE analyses [J].

Randazzo, Cinzia L. ;

Vaughan, Elaine E. ;

Caggia, Cinzia .

INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY, 2006, 109 (1-2) :1-8

[38] Specific PGR primers to identify arbuscular mycorrhizal fungi within colonized roots [J].

Redecker, D .

MYCORRHIZA, 2000, 10 (02) :73-80

[39] Molecular identification of arbuscular mycorrhizal fungi in roots: Perspectives and problems [J].

Redecker, D ;

Hijri, I ;

Wiemken, A .

FOLIA GEOBOTANICA, 2003, 38 (02) :113-124

[40] Ribosomal RNA gene sequence diversity in arbuscular mycorrhizal fungi (Glomeromycota) [J].

Rodriguez, A ;

Clapp, JP ;

Dodd, JC .

JOURNAL OF ECOLOGY, 2004, 92 (06) :986-989

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