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Direct amplification of nodD from community DNA reveals the genetic diversity of Rhizobium leguminosarum in soil

Zeze, A, Mutch, L A and Young, J P W (2001) Direct amplification of nodD from community DNA reveals the genetic diversity of Rhizobium leguminosarum in soil. Environmental Microbiology. pp. 363-370. ISSN 1462-2912

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Abstract

Sequences of nodD, a gene found only in rhizobia, were amplified from total community DNA isolated from a pasture soil. The polymerase chain reaction (PCR) primers used, Y5 and Y6, match nodD from Rhizobium leguminosarum biovar trifolii, R. leguminosarum biovar viciae and Sinorhizobium meliloti. The PCR product was cloned and yielded 68 clones that were identified by restriction pattern as derived from biovar trifolii [11 restriction fragment length polymorphism (RFLP) types] and 15 clones identified as viciae (seven RFLP types). These identifications were confirmed by sequencing. There were no clones related to S. meliloti nodD. For comparison, 122 strains were isolated from nodules of white clover (Trifolium repens) growing at the field site, and 134 from nodules on trap plants of T. repens inoculated with the soil. The nodule isolates were of four nodD RFLP types, with 77% being of a single type. All four of these patterns were also found among the clones from soil DNA, and the same type was the most abundant, although it made up only 34% of the trifolii-like clones. We conclude that clover selects specific genotypes from the available soil population, and that R. leguminosarum biovar trifolii was approximately five times more abundant than biovar viciae in this pasture soil, whereas S. meliloti was rare.

Item Type: Article
Copyright, Publisher and Additional Information: © 2001 Blackwell Science Ltd. This is an electronic version of an article published in Environmental Microbiology: complete citation information for the final version of the paper, as published in the print edition of Molecular Ecology, is available on the Blackwell Synergy online delivery service, accessible via the journal's website at http://www.blackwellpublishing.com/journal.asp?ref=1462-2912 or www.blackwell-synergy.com
Keywords: 16S RIBOSOMAL-RNA, LENGTH-POLYMORPHISM ANALYSIS, BIOVAR VICIAE POPULATIONS, ALFALFA MEDICAGO-SATIVA, NATURAL-POPULATIONS, ENZYME POLYMORPHISM, PHASEOLUS-VULGARIS, LOTUS-CORNICULATUS, WHITE CLOVER, BV TRIFOLII
Institution: The University of York
Academic Units: The University of York > Biology (York)
Depositing User: Peter Young
Date Deposited: 22 Apr 2005
Last Modified: 14 Oct 2014 18:01
Published Version: http://dx.doi.org/10.1046/j.1462-2920.2001.00202.x
Status: Published
Refereed: Yes
Related URLs:
URI: http://eprints.whiterose.ac.uk/id/eprint/411

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