Change in Land Use Alters the Diversity and Composition of Bradyrhizobium Communities and Led to the Introduction of Rhizobium etli into the Tropical Rain Forest of Los Tuxtlas (Mexico)

Abstract

Nitrogen-fixing bacteria of the Bradyrhizobium genus are major symbionts of legume plants in American tropical forests, but little is known about the effects of deforestation and change in land use on their diversity and community structure. Forest clearing is followed by cropping of bean (Phaseolus vulgaris) and maize as intercropped plants in Los Tuxtlas tropical forest of Mexico. The identity of bean-nodulating rhizobia in this area is not known. Using promiscuous trap plants, bradyrhizobia were isolated from soil samples collected in Los Tuxtlas undisturbed forest, and in areas where forest was cleared and land was used as crop fields or as pastures, or where secondary forests were established. Rhizobia were also trapped by using bean plants. Bradyrhizobium strains were classified into genospecies by dnaK sequence analysis supported by recA, glnII and 16S-23S rDNA IGS loci analyses. A total of 29 genospecies were identified, 24 of which did not correspond to any described taxa. A reduction in Bradyrhizobium diversity was observed when forest was turned to crop fields or pastures. Diversity seemed to recover to primary forest levels in secondary forests that derived from abandoned crop fields or pastures. The shifts in diversity were not related to soil characteristics but seemingly to the density of nodulating legumes present at each land use system (LUS). Bradyrhizobium community composition in soils was dependent on land use; however, similarities were observed between crop fields and pastures but not among forest and secondary forest. Most Bradyrhizobium genospecies present in forest were not recovered or become rare in the other LUS. Rhizobium etli was found as the dominant bean-nodulating rhizobia present in crop fields and pastures, and evidence was found that this species was introduced in Los Tuxtlas forest.

Abundance and Diversity of Soybean-Nodulating Rhizobia in Black Soil Are Impacted by Land Use and Crop Management

“…In the present study, the population abundances, community structures, and diversity of effective soybean rhizobia varied drastically among the treatments ( Fig. 1 and Table 1), reflecting the fact that the rhizobia were strongly affected by soil management, like the cropping system, land use patterns, and fertilizer input, which were similar in some respects to previous reports (12,58,60) and also provided some new information.…”

“…Second, the other treatments, except for GL, had lower diversity indexes, and no Bradyrhizobium sp. II bacteria were isolated (Table 1), demonstrating that mowing grass or converting grassland to agricultural use decreased the diversity of soybean rhizobia, which was similar to the effects of deforestation on native Bradyrhizobium communities (60). Third, fertilization did not change the genospecies composition of soybean rhizobia but decreased the diversity of the rhizobia, as shown by the increased relative proportion of Bradyrhizobium sp.…”

Rhizobia Indigenous to the Okavango Region in Sub-Saharan Africa: Diversity, Adaptations, and Host Specificity

“…Reports on B. pachyrhizi are rare, and not much is yet known about its distribution and ecology. A high proportion of B. pachyrhizi bacteria was detected under different land use systems in Mexican tropics using cowpea and siratro (Macroptilium atropurpureum) as trap plants (56). The Mexican sampling sites were characterized by a warm, humid climate and acid soils (pH 4 to 6), strikingly matching the warm, semihumid climate with an annual mean rainfall of 987 mm and an annual mean temperature of 20.4°C (57) in the Cusseque area.…”

Genomic basis of symbiovar mimosae in Rhizobium etli

“…Such genes are present in sv. tropici strains that are also Leucaena symbionts [10]. Like R. etli strain CFN42, Mim1 may produce nodulation factors bearing carbamoyl groups at their non reducing end residues but the position of these decorations must differ because their pSyms encoded distinct carbamoyl transferases, NolO in CFN42 and NodU in Mim1.…”

“…phaseoli and not in sv. mimosae served as a molecular basis to distinguish these symbiovars [10, 11]. Phylogenies indicated that symbiovar mimosae and phaseoli nifH genes were related [9] and similar to the corresponding gene in sv.…”