A Genomic Encyclopedia of the Root Nodule Bacteria: assessing genetic diversity through a systematic biogeographic survey

Abstract

Root nodule bacteria are free-living soil bacteria, belonging to diverse genera within the Alphaproteobacteria and Betaproteobacteria, that have the capacity to form nitrogen-fixing symbioses with legumes. The symbiosis is specific and is governed by signaling molecules produced from both host and bacteria. Sequencing of several model RNB genomes has provided valuable insights into the genetic basis of symbiosis. However, the small number of sequenced RNB genomes available does not currently reflect the phylogenetic diversity of RNB, or the variety of mechanisms that lead to symbiosis in different legume hosts. This prevents a broad understanding of symbiotic interactions and the factors that govern the biogeography of host-microbe symbioses.Here, we outline a proposal to expand the number of sequenced RNB strains, which aims to capture this phylogenetic and biogeographic diversity. Through the Vavilov centers of diversity (Proposal ID: 231) and GEBA-RNB (Proposal ID: 882) projects we will sequence 107 RNB strains, isolated from diverse legume hosts in various geographic locations around the world. The nominated strains belong to nine of the 16 currently validly described RNB genera. They include 13 type strains, as well as elite inoculant strains of high commercial importance. These projects will strongly support systematic sequence-based studies of RNB and contribute to our understanding of the effects of biogeography on the evolution of different species of RNB, as well as the mechanisms that determine the specificity and effectiveness of nodulation and symbiotic nitrogen fixation by RNB with diverse legume hosts.

Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS

“…Most of the selected RNB were part of the DoE Joint Genome Institute's (JGI) international Genomic Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project that aimed to systematically sequence the genomes of diverse rhizobial strains (Reeve et al 2014). The remaining strains were well-studied bacteria whose genomes have previously been sequenced.…”

The Structure and Evolution of Beta-Rhizobial Symbiotic Genes Deduced from Their Complete Genomes

“…between two Burkholderia strains (99.9% similarity) and three Sinorhizobium strains (97.4%) which suggests strongly that the gene transfer often occurred within the same phylogenetic lineages. A unique origin of common nod genes and their horizontal transfer from Alpha-to Betaproteobacteria has been hypothesized i.e., the Alpha-rhizobial origin of nodulation genes [5,30,55,59,78,79,82]. This is supported by the papilionoideae-nodulating Beta-rhizobial strain B. tuberum STM678…”

“…In addition, R. leguminosarum has two nodT genes, which it shares with three Burkholderia strains, which is interesting in consideration that Rhizobium strains are often isolated from Mimosa pudica e.g. R. etli, R. tropici, R. leucaenae, R. mesoamericanum and R. altiplani [31,35,59,73,74]. Moreover, the Mimosa-nodulating R. etli sv.…”

“…This demonstrates that the nod genes evolved according to geographical and host factors, and are the basis of the symbiovar concept which states that it is the mobile nod genes and not the core genome which determines host range in Rhizobia [59]. The genome sequence of B. phymatum STM815 T has recently been published [38], and this shows that it has some similarities with C. taiwanensis in the structure of its symbiotic genes [55].…”

Genomics of Specificity in the Symbiotic Interaction between Rhizobium leguminosarum and Legumes

“…RL has a multi-partite genome, in the form of one large, circular chromosome (4-5Mb) and a variable number (1-6) of large or very large plasmids ( Figure I.4) (Young et al, 2006, Reeve et al, 2010a, Reeve et al, 2010b, Reeve et al, 2015. Some of these resemble chromosomes in their size and functional complexity, and are known as "chromids" .…”