Vol.:(0123456789) 1 3 Current Microbiology https://doi.org/10.1007/s00284-020-02101-4 Methylobacterium symbioticum sp. nov., a new species isolated from spores of Glomus iranicum var. tenuihypharum Jose Antonio Pascual 1  · Margarita Ros 1  · Jesus Martínez 2  · Francisco Carmona 2  · Antonio Bernabé 2  · Rocío Torres 2  · Teresa Lucena 3  · Rosa Aznar 3  · David R. Arahal 3  · Felix Fernández 2 Received: 12 March 2020 / Accepted: 18 June 2020 © Springer Science+Business Media, LLC, part of Springer Nature 2020 Abstract Strain SB0023/3  T , isolated from spores of the arbuscular mycorrhizal fungus Glomus iranicum var. tenuihypharum, was analysed to determine whether it represents a new species. It was studied for its applicability in the field of agriculture to reduce the input of nitrogen fertilizers. Comparative analysis of the 16S rRNA gene sequence shows the strain to be affiliated to the genus Methylobacterium, the closest similarities (98.7%) being shared with Methylobacterium dankookense. Further phylogenomic analysis through Up-to-date Bacterial Core Gene (UBCG) confirmed Methylobacterium dankookense as its closest relative. Average Nucleotide Identity (ANI) and in silico DNA–DNA hybridization (DDH) were lower than 92% and 44%, respectively, of the values shown by its phylogenetic relatives. Its genome had an approximate length of 6.05 Mb and the G + C content of the genome was 70.1 mol%. The main cellular fatty acid was Summed Feature 8 (C 18:1 ω7c and/or C 18:1 ω6c). It is a Gram-staining-negative, pink-pigmented, strictly aerobic and facultative methylotroph; it grows at 28 ºC and can grow at up to 3% salinity in the presence of sodium chloride. All the data collected support the naming of a novel species to accommodate the strain SB0023/3  T , for which the name Methylobacterium symbioticum sp. nov. is proposed. The type strain is SB0023/3  T (=CECT 9862  T =PYCC 8351  T ). Abbreviations AMF Arbuscular mycorrhizal fungi ANI Average Nucleotide Identity BLAST Basic Local Alignment Search Tool UBCG Up-to-date Bacterial Core Gene CECT Colección Española de Cultivos Tipo DDH DNA–DNA hybridization SCSIE Servicio Central de Soporte a la Investigación Experimental GGDC Genome-to-Genome Distance Calculator GSI Gene Support Index NCBI National Center for Biotechnology Information PYCC Portuguese Yeast Culture Collection RAST Rapid Annotation using Subsystem Technology SPAD Soil–Plant Analyses Development Introduction Arbuscular mycorrhizal fungi (AMF) are obligate plant symbionts that are able to colonize the roots of approxi- mately two-thirds of all terrestrial plant species [1]. Glomus iranicum var. tenuihypharum is an AMF isolated from alka- line soil with high concentrations of Ca +2 , Na + and Mg +2 , a low C/N ratio and low organic matter level [2]. This isolate induces a high plant biomass, leading to higher yields, not only in leafy crops but also in fruit crops [1]. This benefi- cial effect be attributed to its ability to permit higher plant nutrient and water uptake probably through the increase in hydraulic conductivity [3]. However, although an extensive literature exists on rhizosphere colonization, little is known regarding the bacterial colonization of AMF hyphae (the ‘hyphosphere’). Bacteria and AMF have different interac- tion ways [4]. It has also reported interactive effects between pathogens, rhizobia and AMF [5, 6]. Moreover, bacteria The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene and whole genome sequences of the type strain of Methylobacterium symbioticum are MN154398 and GCA_902141845, respectively. * Jose Antonio Pascual jpascual@cebas.csic.es 1 Departamento de Conservación de Suelos, Agua y Manejo de Residuos Orgánicos, CEBAS-CSIC, Murcia, Spain 2 Symborg SL, Murcia, Spain 3 Departamento de Microbiología y Ecología, y Colección Española de Cultivos Tipo (CECT), Universitat de València, València, Spain