A novel plant growth-promoting rhizobacterium, Rhizosphaericola mali gen. nov., sp. nov., isolated from healthy apple tree soil

The rhizosphere microbial community is closely associated with plant disease by regulating plant growth, agricultural production, nutrient availability, plant hormone and adaptation to environmental changes. Therefore, it is very important to identify the rhizosphere microbes around plant roots and understand their functions. While studying the differences between the rhizosphere microbiota of healthy and diseased apple trees to find the cause of apple tree disease, we isolated a novel strain, designated as B3-10T, from the rhizosphere soil of a healthy apple tree. The genome relatedness indices between strain B3-10T and other type species of family Chitinophagaceae were in the ranges of 62.4–67.0% for ANI, 18.6–32.1% for dDDH, and 39.0–56.6% for AAI, which were significantly below the cut‑off values for the species delineation, indicating that strain B3-10T could be considered to represent a novel genus in family Chitinophagaceae. Interestingly, the complete genome of strain B3-10T contained a number of genes encoding ACC-deaminase, siderophore production, and acetoin production contributing to plant-beneficial functions. Furthermore, strain B3-10T was found to significantly promote the growth of shoots and roots of the Nicotiana benthamiana, which is widely used as a good model for plant biology, demonstrating that strain B3-10T, a rhizosphere microbe of healthy apple trees, has the potential to promote growth and reduce disease. The phenotypic, chemotaxonomic, phylogenetic, genomic, and physiological properties of this plant growth-promoting (rhizo)bacterium, strain B3-10T supported the proposal of a novel genus in the family Chitinophagaceae, for which the name Rhizosphaericola mali gen. nov., sp. nov. (= KCTC 72123T = NBRC 114178T).

Forward CDS, region that is not CDS is described as blank; Reverse CDS, region that is not CDS is described as blank; tRNA, Region of tRNA is marked in light green; rRNA, Region of rRNA is marked in red; GC content, Region that has higher value of GC percentage than that of average is described in exterior light green peak.
Region that has lower value of GC percentage than that of average is described in interior lavender peak.Height of the peak describes the difference from the average GC percentage.; GC skew, According to the formula, (G-C)/(G+C), positive value shows that G is dominant while negative value shows that C is dominant.The exterior light green peak describes the region that has higher G content while interior lavender peak describes the region that higher C content.

Fig. S1
Fig. S1 Maximum-likelihood (a) and maximum-parsimony (b) trees showing the phylogenetic relationships between strain B3-10 T and their closely related taxa, based on 16S rRNA gene sequences.Bootstrap values over 50% are shown on the nodes as percentages of 1,000 replicates.Fodinibius salinus YIM D17 T was used as an outgroup.
speE involved in Polyamines biosynthesis.O-methyltransferase. Catalyzes the production of spermidine from putrescine and decarboxylated S-adenosylmethionine (dcSAM), which acts as an aminopropyl donor.speH involved in Polyamines biosynthesis.Catalyzes the decarboxylation of S-adenosylmethionine to S-adenosylmethioninamine (dcAdoMet).Propylamine donor required for synthesis of polyamines spermine and spermidine from diamine putrescine metK involved in Polyamines biosynthesis.Catalyzes the formation of S-adenosylmethionine from methionine and ATP kdpAThe components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions kdpB The components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions kdpC The components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions kdpD The components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions.Histidine kinaseResistance to drugs and heavy metals fetA Involved in tetracycline resistance.Omologs of the multifunctional tetracycline-metal/ABC transporter complex ModABC involved in molybdenum import.Responsible for energy coupling to the transport system exbB MotA TolQ exbB proton channel copA Involved in copper resistance.Multicopper oxidase arsH Involved in Arsenic resistance.Nadph-dependent fmn reductase.arsenical resistance protein ArsH arsC Involved in Arsenic resistance.Arsenate reductase arsR Involved in Arsenic resistance.arsR family transcriptional regulator cusR Involved in copper/silver resistance.RegulatoR, two-component system, OmpR family, copper resistance cusS Involved in copper/silver resistance.Histidine kinase, two-component system, OmpR family, heavy metal sensor czcA Involved in cobalt/zinc/cadmium resistance.Heavy metal efflux pump and cobalt-zinccadmium resistance protein CzcA czcB Involved in cobalt/zinc/cadmium resistance.Efflux transporter rnd family, mfp subunit.Cobaltzinc-cadmium resistance protein CzcB ompW Involved in cobalt/zinc/cadmium resistance.Outer membrane protein Plant protection from stress PaaE Plant protection from nitrosative stress.Is involved in NO detoxification in an aerobic process, termed nitric oxide dioxygenase (NOD) reaction that utilizes O(2) and NAD(P)H to convert NO to nitrate sodA Plant protection from oxidative stress.Superoxide dismutases.Destroys radicals which are normally produced within the cells and which are toxic to biological systems katEG Plant protection from oxidative stress.Bifunctional enzyme with both catalase and broadspectrum peroxidase activity.ahpC Plant protection from oxidative stress.Alkyl hydroperoxide reductase ahpF Plant protection from oxidative stress.Thioredoxin reductase ahpD Plant protection from oxidative stress.Antioxidant protein with alkyl hydroperoxidase activity.Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity tpx Plant protection from oxidative stress.Could remove peroxides or H(2)O(2) ggt Plant protection from oxidative stress.gamma-glutamyl transpeptidas ohrAR Plant protection from oxidative stress.Resistance to organic peroxides soxS Plant protection from oxidative stress.oxyR Plant protection from oxidative stress.

The table can be viewed in the separately attached Excel file.
Supplementary TableS4Morphological and physiological characteristics between strain B3-10 T and other type species in the family Chitinophagaceae Supplementary TableS5Cellular fatty acid profiles (% of total) of strain B3-10 T and the type strains of closely related members of the family Chitinophagaceae Values are percentages of total fatty acids.Data are from this study.Fatty acid are listed using standard abbreciations (number of carbon atoms: number of double bonds).Summed features represent two or three fatty acids that cannot be separated by GLC using the MIDI system.Summed Feature3 comprised Various PGP-related genes found in the genome of strain B3-10 T T .All data were obtained in this study.+, Positive; w, weakly positive; -, negative.et al. 2017); 48, (Qu and Yuan 2008); 49, (An et al. 2007); 50, (Zhang et al. 2013); 51, (Xie and Yokota 2006); 52, (Anders et al. 2014) DPG, diphosphatidylglycerol; PE, phosphatidylethanolamine; PG, phosphatidylglycerol; PIM, phosphatidyl-inositolmannosides; AGL, aminoglycolipid; PG, phosphatidylglycerol, GPL, glycophospholipid ; AGL, aminoglycolipid ; APL, aminophospholipid; AL, unidentified aminolipids; PL, unidentified phospholipid; L, unidentified lipids; -, not detected.*