Genetic identification of potential nodulating bacteria and nodule-associated bacteria (NAB) within root nodules of Inga punctata trees in a Costa Rican Cloud Forest

Abstract

Background and Aims Leguminous tree root nodules have N-fixing, nodulating bacteria important for soil C and N cycle recovery following forest disturbance, and nodule-associated bacteria (NAB), which often provide plant growth promoting (PGP) activities. However, composition and function of these microbiomes within tropical leguminous forest trees is understudied. Methods Root nodules were collected from 1, 2, 13-year-old and old growth Inga punctata trees within a tropical cloud forest. Nodule DNA was extracted, from which bacterial taxa were identified through Illumina DNA sequencing methods. Results Bradyrhizobium diazoefficiensDNA sequences represented 63% to 86% and NAB sequences represented 7% to 12% of the total bacterial taxa in the nodules. Collectively, 26 of the NAB taxa were identified with 9 PGP activities. The 1 year-old nodules had the greatest percentages of PGP NAB taxa, which decreased with tree age, though the percentage of total NAB DNA increased with tree age, as did the NAB community complexity. Conclusions Bradyrhizobium diazoefficiensappears to be the root nodule-forming bacteria, while the NAB genera with known PGP activities appear to provide important functions that benefit both the nodule microbiome and I. punctata. The greater percentage of PGP NAB in the youngest nodules suggests their importance in early growth and development of I. punctata and its root nodules, the great presence of NAB DNA in all nodules suggests the importance of NAB throughout the lifespan of I. punctata, and the increasing NAB community complexity with tree age suggests the microbiome undergoes parallel succession with the tree.