Genetic Structure of Rhizobium leguminosarum biovar trifolii and viciae Populations Found in Two Oregon Soils under Different Plant Communities

Abstract

An investigation was carried out to determine the genetic structure in soil populations of Rhizobium kguminosarum bv. trifolii and viciae at each of two Oregon sites (A and C) that were 1 km apart. Although the soils were similar, the plant communities were quite different because grazing by domestic animals had been allowed (site A) or prevented (site C). Analysis of allelic variation at 13 enzyme-encoding loci by multilocus enzyme electrophoresis delineated 202 chromosomal types (ETs) among a total of 456 isolates representing two populations of R. kguminosarum bv. trifolii (AT and CT) and two populations of R. leguminosarum bv. viciae (AV and CV). Regardless of their site of origin or biovar affiliation, isolates of the same ET were confirmed to be more closely related to each other than to isolates of other ETs by repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus sequences and the PCR technique. Despite the wide range in densities of the Rhizobium populations (<102 to >105/g of soil), their overall genetic diversities were similar (mean genetic diversity, 0.45 to 0.51), indicating that low-density populations of soil-borne bacterial species are not necessarily of little genetic diversity. Linkage disequilibrium analysis revealed significant multilocus structure (nonrandom associations of alleles) within each of the four populations. From a combination of cluster and linkage disequilibrium analyses, a total of eight distinct groups of ETs were defined in the four populations. Two groups (I and III) contributed significant numbers of ETs and isolates to each population. The two populations of R. leguminosarum bv. viciae (AV and CV) exhibited similar genetic structures despite existing at different densities, in different plant communities, and in the presence (CV) or absence (AV) of their local Vcia hosts. In contrast, total linkage disequilibrium was partitioned differently in two biovar populations occupying the same soil (AV and AT), with disequilibrium in the latter being due entirely to the presence of group V.

Genetic diversity of an Italian Rhizobium meliloti population from different Medicago sativa varieties

“…The population genetics of these genera has been studied, and almost all of the data reported previously indicate that there is a high level of genetic diversity in these bacteria. This genetic diversity has been associated with a strong linkage disequilibrium (8,9,11,12,31,47) or no linkage disequilibrium (3,8,12,27,40,41), which provides evidence of genetic exchange in the population considered (46). In general, the results of studies of the genetic structures of natural soil populations support the hypothesis that recombination may play a role in generating new genotypes, since these populations are very different in the genetic structure from bacterial populations recovered from outbreaks of infectious diseases, which are typically clonal (10,46).…”

“…Most studies of the population genetics of Rhizobium and Bradyrhizobium species have been carried out by using serological or multilocus enzyme electrophoresis techniques (3,8,9,11,12,28,(40)(41)(42). More recently, techniques based on DNA analysis have been used with or instead of multilocus enzyme electrophoresis (4, 7, 9, 12, 24-27, 45, 47).…”

Grain Legumes in Northern Great Plains: Impacts on Selected Biological Soil Processes

“…The distribution and diversity of specific strains of N 2 –fixing bacteria vary with environmental conditions and presence or absence of legume hosts (Strain et al, 1994). Management, the environment, as well as the plant community, can influence Rhizobium , and thus impact the diversity of this group of microorganisms (Turco and Bezdicek, 1987; Hirsch et al, 1993; Strain et al, 1994; Ferreira et al, 2000). Crop rotations in Brazil containing soybean resulted in higher populations and greater diversity and activity of Bradyrhizobium than those without soybean, even though more than 15 yr had passed since inoculation (Ferreira et al, 2000).…”

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

“…Because this is very convenient, nearly all studies of rhizobia have started from cultures derived from root nodules. This includes numerous studies of genetic diversity, using methods such as enzyme electrophoresis (Young, 1985; Young et al ., 1987; Harrison et al ., 1989; Leung et al ., 1994), restriction fragment length polymorphism (RFLP; Young and Wexler, 1988; Kaijalainen and Lindström, 1989; Demezas et al ., 1991) or polymerase chain reaction (PCR)‐based techniques (Harrison et al ., 1992; Amarger et al ., 1994; Laguerre et al ., 1994; Leung et al ., 1994; Strain et al ., 1994; Eardly et al ., 1995; Haukka et al ., 1996; Turner et al ., 1996). We have learned a great deal from this work, but it must be recognized that the diversity sampled in this way has been ‘filtered’ by the plant hosts.…”