Isolation, Characterization, and Complete Genome Sequence of a Bradyrhizobium Strain Lb8 From Nodules of Peanut Utilizing Crack Entry Infection.

Dev Paudel,Karen Kelley,Stephanie Maya,Ze Peng,Liping Wang,Jianping Wang,Jean-Michel Ané,Fengxia Liu,Matthew Crook

doi:10.3389/fmicb.2020.00093

Dev Paudel, Karen Kelley + Show 7 more

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https://doi.org/10.3389/fmicb.2020.00093

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Abstract

In many legumes, the colonization of roots by rhizobia is via “root hair entry” and its molecular mechanisms have been extensively studied. However, the nodulation of peanuts (Arachis hypogaea L.) by Bradyrhizobium strains requires an intercellular colonization process called “crack entry,” which is understudied. To understand the intercellular crack entry process, it is critical to develop the tools and resources related to the rhizobium in addition to focus on investigating the mechanisms of the plant host. In this study, we isolated a Bradyrhizobium sp. strain, Lb8 from peanut root nodules and sequenced it using PacBio long reads. The complete genome sequence was a circular chromosome of 8,718,147 base-pair (bp) with an average GC content of 63.14%. No plasmid sequence was detected in the sequenced DNA sample. A total of 8,433 potential protein-encoding genes, one rRNA cluster, and 51 tRNA genes were annotated. Fifty-eight percent of the predicted genes showed similarity to genes of known functions and were classified into 27 subsystems representing various biological processes. The genome shared 92% of the gene families with B. diazoefficens USDA 110T. A presumptive symbiosis island of 778 Kb was detected, which included two clusters of nif and nod genes. A total of 711 putative protein-encoding genes were in this region, among which 455 genes have potential functions related to symbiotic nitrogen fixation and DNA transmission. Of 21 genes annotated as transposase, 16 were located in the symbiosis island. Lb8 possessed both Type III and Type IV protein secretion systems, and our work elucidated the association of flagellar Type III secretion systems in bradyrhizobia. These observations suggested that complex rearrangement, such as horizontal transfer and insertion of different DNA elements, might be responsible for the plasticity of the Bradyrhizobium genome.

Highlights

Rhizobia are soil-borne bacteria that colonize plant tissues interor intra-cellularly and trigger the development of new organs called nodules, which generally happens on legume roots
Nodules were seen on the roots of all peanut plants inoculated with the five strains separately, at 13 days after inoculation (DAI) (Supplementary Figure 2A)
Many Bradyrhizobium sp. can nodulate peanuts, where a high degree of correlation exists between nitrogenase activity and shoot weight, nodule number, nodule mass, and total nitrogen (Wynne et al, 1983; Nigam et al, 1985; Li et al, 2015, 2019)

Summary

Introduction

Rhizobia are soil-borne bacteria that colonize plant tissues interor intra-cellularly and trigger the development of new organs called nodules, which generally happens on legume roots. Inside of these nodules, the rhizobia differentiate into bacteroids and convert N2 gas into ammonium (Oldroyd and Downie, 2008; Kuever et al, 2015; Ormeño-Orrillo et al, 2015; Peix et al, 2015; Mus et al, 2016). This intercellular infection is considered an evolutionarily ancient invasion mechanism (Groth et al, 2010; Madsen et al, 2010), which might be a key to facilitate transforming non-legumes for biological nitrogen fixation via symbiosis (Charpentier and Oldroyd, 2010)

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