Evolution of Diverse Effective N ₂ -Fixing Microsymbionts of Cicer arietinum following Horizontal Transfer of the Mesorhizobium ciceri CC1192 Symbiosis Integrative and Conjugative Element

Abstract

Rhizobia are soil bacteria capable of forming N₂-fixing symbioses with legumes, with highly effective strains often selected in agriculture as inoculants to maximize symbiotic N₂ fixation. When rhizobia in the genus <i>Mesorhizobium</i> have been introduced with exotic legumes into farming systems, horizontal transfer of symbiosis Integrative and Conjugative Elements (ICEs) from the inoculant strain to soil bacteria has resulted in the evolution of ineffective N₂-fixing rhizobia that are competitive for nodulation with the target legume. In Australia, <i>Cicer arietinum</i> (chickpea) has been inoculated since the 1970's with <i>Mesorhizobium ciceri</i> sv. <i>ciceri</i> CC1192, a highly effective strain from Israel. Although the full genome sequence of this organism is available, little is known about the mobility of its symbiosis genes and the diversity of cultivated <i>C. arietinum</i>-nodulating organisms. Here, we show the CC1192 genome harbors a 419-kb symbiosis ICE (ICE<i>Mc</i>Sym¹¹⁹²) and a 648-kb <i>repABC</i>-type plasmid pMC1192 carrying putative <i>fix</i> genes. We sequenced the genomes of 11 <i>C. arietinum</i> nodule isolates from a field site exclusively inoculated with CC1192 and showed they were diverse unrelated <i>Mesorhizobium</i> carrying ICE<i>Mc</i>Sym¹¹⁹², indicating they had acquired the ICE by environmental transfer. No exconjugants harboured pMc1192 and the plasmid was not essential for N₂ fixation in CC1192. Laboratory conjugation experiments confirmed ICE<i>Mc</i>Sym¹¹⁹² is mobile, integrating site-specifically within the 3' end of one of the four <i>ser-</i>tRNA genes in the R7ANS recipient genome. Strikingly, all ICE<i>Mc</i>Sym¹¹⁹² exconjugants were as efficient at fixing N₂ with <i>C. arietinum</i> as CC1192, demonstrating ICE transfer does not necessarily yield ineffective microsymbionts as previously observed.<b>Importance</b> Symbiotic N₂ fixation is a key component of sustainable agriculture and in many parts of the world legumes are inoculated with highly efficient strains of rhizobia to maximise fixed N₂ inputs into farming systems. Symbiosis genes for <i>Mesorhizobium</i> spp. are often encoded chromosomally within mobile gene clusters called Integrative and Conjugative Elements or ICEs. In Australia, where all agricultural legumes and their rhizobia are exotic, horizontal transfer of ICEs from inoculant <i>Mesorhizobium</i> strains to native rhizobia has led to the evolution of inefficient strains that outcompete the original inoculant, with the potential to render it ineffective. However, the commercial inoculant strain for <i>Cicer arietinum</i> (chickpea), <i>M. ciceri</i> CC1192, has a mobile symbiosis ICE (ICE<i>Mc</i>Sym¹¹⁹²) which can support high rates of N₂ fixation following either environmental or laboratory transfer into diverse <i>Mesorhizobium</i> backgrounds, demonstrating ICE transfer does not necessarily yield ineffective microsymbionts as previously observed.