High-quality permanent draft genome sequence of Ensifer medicae strain WSM244, a microsymbiont isolated from Medicago polymorpha growing in alkaline soil.

Julie Ardley,Natalia Ivanova,Graham O’Hara,T B K Reddy,Tanja Woyke,Wayne Reeve,Rekha Seshadri,John Howieson,Nikos Kyrpides,Victor Markowitz,Rui Tian,Amrita Pati

doi:10.1186/s40793-015-0119-5

Abstract

Ensifer medicae WSM244 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago species. WSM244 was isolated in 1979 from a nodule recovered from the roots of the annual Medicago polymorpha L. growing in alkaline soil (pH 8.0) in Tel Afer, Iraq. WSM244 is the only acid-sensitive E. medicae strain that has been sequenced to date. It is effective at fixing nitrogen with M. polymorpha L., as well as with more alkaline-adapted Medicago spp. such as M. littoralis Loisel., M. scutellata (L.) Mill., M. tornata (L.) Mill. and M. truncatula Gaertn. This strain is also effective with the perennial M. sativa L. Here we describe the features of E. medicae WSM244, together with genome sequence information and its annotation. The 6,650,282 bp high-quality permanent draft genome is arranged into 91 scaffolds of 91 contigs containing 6,427 protein-coding genes and 68 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.Electronic supplementary materialThe online version of this article (doi:10.1186/s40793-015-0119-5) contains supplementary material, which is available to authorized users.

Highlights

Root nodule bacteria that fix atmospheric nitrogen in association with annual and perennial pasture legumes have important roles in agriculture
This strain was superior in N2-fixation on a range of medics (M sativa L., M truncatula Gaertn., M. tornata L., M. polymorpha L., M. littoralis Loisel., M scutellata (L.) Mill.) in glasshouse tests in Australia and field trials in Iraq in 1980, and was Ardley et al Standards in Genomic Sciences (2015) 10:126 recommended for development as an inoculant in Iraq
This is in contrast to other E. medicae strains, which typically are the dominant microsymbiont partners of annual medics growing on acid soils, in contrast to the more acid-sensitive E. meliloti, which preferentially associates with alkaline-soil-adapted Medicago spp

Summary

Introduction

Root nodule bacteria that fix atmospheric nitrogen in association with annual and perennial pasture legumes have important roles in agriculture. Ensifer medicae WSM244 was isolated in 1979 from a root nodule of M. polymorpha L. growing on alkaline soil (pH 8.0) near Tel Afer, Iraq [6] This strain was superior in N2-fixation on a range of medics (M sativa L., M truncatula Gaertn., M. tornata L., M. polymorpha L., M. littoralis Loisel., M scutellata (L.) Mill.) in glasshouse tests in Australia and field trials in Iraq in 1980, and was Ardley et al Standards in Genomic Sciences (2015) 10:126 recommended for development as an inoculant in Iraq WSM244 contains the tcsA-tcrA-fsrR- regulatory gene cluster which is required for the low-pH-activation of lpiA and acvB in E. medicae WSM419 [36] This finding is in direct contrast to the absence of fsrR, tcsA and tcrA in the the acid-sensitive strain E. meliloti 1021. This suggests that either there may be differences in pH responsive gene expression in the WSM244 background, or that acid tolerant E. medicae strains possess other candidate genes that are required for low pH adaptation and have not yet been identified

Conclusions

Findings

52. Biological Agents