The complete genome sequence of Ensifer meliloti strain CCMM B554 (FSM-MA), a highly effective nitrogen-fixing microsymbiont of Medicago truncatula Gaertn

Nagymihály et al. Standards in Genomic Sciences (2017) 12:75 DOI 10.1186/s40793-017-0298-3 EXTENDED GENOME REPORT Open Access The complete genome sequence of Ensifer meliloti strain CCMM B554 (FSM-MA), a highly effective nitrogen-fixing microsymbiont of Medicago truncatula Gaertn Marianna Nagymihály1,2, Bálint M. Vásarhelyi3, Quentin Barrière2, Teik-Min Chong4,5, Balázs Bálint3, Péter Bihari3, Kar-Wai Hong4,5, Balázs Horváth3, Jamal Ibijbijen6, Mohammed Amar7, Attila Farkas1, Éva Kondorosi1, Kok-Gan Chan4,5, Véronique Gruber8, Pascal Ratet8, Peter Mergaert2 and Attila Kereszt1,3* Abstract Strain CCMM B554, also known as FSM-MA, is a soil dwelling and nodule forming, nitrogen-fixing bacterium isolated from the nodules of the legume Medicago arborea L. in the Maamora Forest, Morocco. The strain forms effective nitrogen fixing nodules on species of the Medicago, Melilotus and Trigonella genera and is exceptional because it is a highly effective symbiotic partner of the two most widely used accessions, A17 and R108, of the model legume Medicago truncatula Gaertn. Based on 16S rRNA gene sequence, multilocus sequence and average nucleotide identity analyses, FSM-MA is identified as a new Ensifer meliloti strain. The genome is 6,70 Mbp and is comprised of the chromosome (3,64 Mbp) harboring 3574 predicted genes and two megaplasmids, pSymA (1,42 Mbp) and pSymB (1,64 Mbp) with respectively 1481 and 1595 predicted genes. The average GC content of the genome is 61.93%. The FSM-MA genome structure is highly similar and co-linear to other E. meliloti strains in the chromosome and the pSymB megaplasmid while, in contrast, it shows high variability in the pSymA plasmid. The large number of strain-specific sequences in pSymA as well as strain-specific genes on pSymB involved in the biosynthesis of the lipopolysaccharide and capsular polysaccharide surface polysaccharides may encode novel symbiotic functions explaining the high symbiotic performance of FSM-MA. Keywords: Ensifer meliloti, Root nodule bacteria, Nitrogen-fixation, Symbiosis Introduction To secure their nitrogen supply, legumes such as alfalfa, pea, (soy−/faba-)bean establish an endosymbiotic interaction with soil bacteria collectively called rhizobia that can reduce atmospheric nitrogen gas and produce reduced nitrogen molecules metabolizable by the plants. This symbiosis between legumes and rhizobia is of ecological and economic importance because of its contribution to the global nitrogen cycle, its impact on sustainable agriculture * Correspondence: ; 1 Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary 3 Seqomics Biotechnology Ltd, Mórahalom, Hungary Full list of author information is available at the end of the article and its biotechnological potential to ensure nitrogen supply in agriculture [1]. The reduction of atmospheric nitrogen by rhizobia takes place in a specific niche, within the cells of de novo formed organs called nodules found usually on the roots and in some cases on the stem of the plants. Nodule development is initiated when flavonoids released by the plants induce the expression of the bacterial nodulation (nod) genes resulting in the production of the lipo-chitooligosaccharide signal molecules, the Nod factors. Nod factors cause a change in the direction of polar growth in developing root hairs and simultaneously induce cell division in the root cortex cells. As a result, a nodule primordium is formed © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Nagymihály et al. Standards in Genomic Sciences (2017) 12:75 that turns into meristematic tissue to produce the cells of the nodule and bacteria become entrapped in the curled root hair where they form an infection pocket. From the site of the infection pocket, a tubular structure, called infection thread, is formed in the root hair that grows toward the cells of the developing nodule. In the infection thread, bacteria multiply and finally they are released into the cytoplasm of the nodule cells via a mechanism resembling endocytosis resulting in organelle-like structures called symbiosomes. Symbiosomes have a membrane of plant origin which surrounds one or more bacteria. After bacterial release, the cells of both partners differentiate into mature symbiotic cells. The nodule cells become enlarged polyploid cells which host several tens of thousands of bacteria that are themselves differentiated into a nitrogenfixing form called bacteroid [2–4]. Interestingly, in Medicago and closely related species like Pisum and Vicia, the host imposes a terminal differentiation on the bacterial partner that is accompanied by the increase in the DNA content and size of the bacteroids and results in the loss of their cell division capacity [5]. This terminal differentiation is orchestrated by nodule-specific cysteine-rich peptides that are expressed exclusively in the infected cells of the nodule [6, 7]. To effectively investigate these interactions, two genetic model legume species, Lotus japonicus (Regel) K. Larsen (bird’s-foot trefoil) and Medicago truncatula Gaertn. (barrel clover/barrel medic) have been chosen for which structural and functional genomics tools and databases have been developed [8, 9]. M. truncatula is a diploid, selfpollinating annual plant belonging to the Medicago genus, which contains species that are among the most extensively cultivated forage and pasture plants. Medicago plants establish symbiosis only with a limited number of bacterial species, mainly with Ensifer (synonym Sinorhizobium) meliloti and Ensifer medicae, and with certain Ensifer fredii strains and Rhizobium mongolense [10–12]. However, some combinations of wild-type plants (species, sub-species and ecotypes) and bacterial strains of the most-studied bacterial species, E. meliloti and E. medicae, often lead to incompatible interactions [13–17], i.e. nodule formation is initiated but bacteria cannot invade nodules or cannot persist and fix nitrogen in the symbiotic organ. The incompatibility can be caused by functions/proteins encoded by genes in the accessory genome of the bacteria [14] such as the strain-specific HrrP peptidase [18], strain specific exopolysaccharide production [19] and/or allelic variants of the host genes like the NFS1 and NFS2 genes encoding NCR peptides in M. truncatula [20, 21]. Strikingly, the model bacterium E. meliloti strain 1021 (with the reference genome and most o (...truncated)