Diversity and Abundance of Populations of Bean-Nodulating Rhizobia as a Function of Liming and Cropping History in Acidic Brazilian Soils

Abstract

The application of lime to acidic soils may provide nutrients and favourable conditions to kick-start the growth of bacterial cells in the short term, while long term alteration due to liming may also have an impact on diversity of naturalised symbiotic rhizobial populations. The aims of this study were: (i) to determine the effects of cropping and liming on the the abundance and survival of beannodulating rhizobia in an acidic soil; (ii) to determine the structure of bean-nodulating populations along gradients of increasing acidity stress in a Brazilian soil subjected to liming and cropped with common bean (Phaseolus vulgaris L.). Rhizobial populations were smallest in soils continuously cropped with rice compared with those cropped with common bean, maize and a soybean/wheat rotation. In the absence of a common bean crop the effects of the soil acidity complex on declines in the size of rhizobia populations were highly significant After incubation rhizobia in an acidic soil sampled from the bean field remained at around 90 to 94% of the initial population in limed soils, (4, 7 and 11% of aluminium saturation), whilst in soils with 27 and 36% of aluminium saturation the abundance declined to about 3 to 7% of that initially observed. Polymerase chain reaction (PCR)-mediated restriction fragment length polymorphism (RFLP) analysis of the 16S-23S rRNA intergenic spacer (IGS) and the 16S rRNA gene indicated that the structure and diversity of the native rhizobia from the bean field was altered due to liming. The population in the unlimed soil had less diversity than in limed soil. Isolates belonging to R. tropici IIB and to R. leguminosarum bv. phaseoli putative species were predominant (49.7% and 32.6%, respectively). The number of isolates/IGS groups within R. leguminosarum bv. phaseoli profiles gave a negative relationship with the number of rhizobia in the soil; whilst with R. tropici IIB the correlation between number of IGS groups within each population and density of rhizobia populations was positive. The expected dominance of R. tropici in the rhizobial population from unlimed soil, hypothesised on the basis of earlier reports of acid tolerance in this species, was not found. Isolates affiliated to R. tropici IIB and to R. leguminosarum bv. phaseoli were predominant in all soil populations (50% and 33%, respectively overall). In the soil which had received liming the R. tropici IIB pattern types contained the highest diversity in terms of the number of IGS groups. In contrast, there was a higher number of R. leguminosarum bv. phaseoli types in the unlimed soil with lowest pH than in the populations from soils with the highest pH. Effects of decreased acidity on increased abundance of rhizobia and diversity of rhizobial populations were found, but there was no clear relationship between tolerance of the rhizobial isolates of acidity in laboratory tests and the acidity of the soil from which they were isolated. The high diversity presented by these indigenous rhizobial populations is unlikely to enhance nitrogen and consequently to improve bean production directly; but this study is the first step in building knowledge that will help us to understand what makes the rhizobia-legume symbiosis with indigenous or selected inoculated strains succeed or fail in the field. The genetic variability demonstrated by bean-nodulating rhizobial populations for small-scale agricultural systems in the tropics could be a useful buffering against soil stresses.