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

Abstract

Article:Zeze, A, Mutch, L A and Young, J P W orcid.org/0000-0001- 5259-4830 (2001) ReuseItems deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. TakedownIf you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing eprints@whiterose.ac.uk including the URL of the record and the reason for the withdrawal request. SummarySequences 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 trifoliilike 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.

Genomics of Specificity in the Symbiotic Interaction between Rhizobium leguminosarum and Legumes

“…Laguerre et al (2003), in their ground-breaking study of plant selection of rhizobial genotypes showed that pea plants did not necessarily select the most abundant genotype in the soil; rather, they were able to discriminate among the diversity of soil rhizobial genotypes. This phenomenon had been already described in an earlier clover study by Zeze et al (2001), and in a pea study by Bromfield et al (1995) as well as for other rhizobia-legume systems (Hartmann et al, 1998). As mentioned above, lentil and fava bean reflect in their nodules a rhizobial population that was not significantly different from soil populations.…”

“…This amounts to a 15x coverage of one single genome, and would be insufficient to study a whole Rlv population (Jorrín and Imperial, 2015a). Other culture-independent methods, such as direct gene amplification from soil DNA (Zeze et al, 2001, Sarita et al, 2005, Ando et al, 2005, necessarily restrict the analysis to the number of chosen markers and limits any analysis of the entire RL soil population. This leaves culture-dependent methods.…”

“…As an example, the cultivation of the host plant has been shown to have a homogenizing effect on rhizobial populations (Hirsch, 1996). Handley et al (1998) It has been proposed that some Rhizobium leguminosarum genotypes could be more adapted to specific plant genera, species or cultivars (Davis et al, 1988, Bromfield et al, 1995, Hartmann et al, 1998, Zeze et al, 2001, Laguerre et al, 2003, Mutch and Young, 2004. We have shown that legume hosts can exhibit a preference for specific rhizobial genotypes out of those present in the soil, and that this selection is dependent on the legume species (Chapter 1) (Jorrín and Imperial, 2015b); this selection is not the same for the different plant species used in this Thesis.…”

“…This particular genomic composition has been interpreted as a strategy to, at the same time, maintain a large amount of genetic information and reduce its generation time to 2-3h (Streit et al, 1991, Jorrín and Imperial, 2015a. , Bromfield et al, 1995, Hartmann et al, 1998, Zeze et al, 2001, Laguerre et al, 2003. This would imply that the plant selects for specific rhizobial genotypes from those present in soil (Jorrín and Imperial, 2015b (Hynes and Oconnell, 1990, Evans et al, 1996, Laguerre et al, 2003, Mutch and Young, 2004).…”

Molecular diversity of berseem (<italic>Trifolium alexandrinum</italic> L.) rhizobia isolated from Haryana soil

“…trifolii is large and well documented in other parts of the world (Zeze et al, 2001;Duodu et al, 2007). In northern India, in the state of Haryana, extreme conditions of temperature and moisture prevails as rains are very scanty and temperature range is high from -3 to 47 °C (Narula et al, 2013).…”