Isolation, Identification and Characterization of Endophytic Bacterium Rhizobium oryzihabitans sp. nov., from Rice Root with Biotechnological Potential in Agriculture

Abstract

A flagellate, rod–shaped bacterium designated strain M15T was isolated from rice roots. Phylogenetic analysis based on the sequences of the 16S rRNA, housekeeping genes and genomes showed that the isolate belonged to the genus Rhizobium, with the highest 16S rRNA similarity to Rhizobium radiobacter LMG140T (99.64%) and Rhizobium pusense NRCPB10T (99.36%), respectively. The complete genome of the strain M15T has a 59.28% G+C content, and the highest average nucleotide identity (ANI) and DNA-DNA relatedness (DDH) values were obtained with R. radiobacter LMG140T (88.11%, 54.80%), R. pusense NRCPB10T (86.00%, 53.00%) and R. nepotum 39/7T (88.80%, 49.80%), respectively. Plant growth-promoting characteristics tests showed that the strain M15T produced siderophore, 1–aminocyclopropane–1–carboxylate (ACC) deaminase and indole-3-acetic acid (IAA) and also produced some secondary metabolites according to the analysis of the comparative genomes. Based on the data mentioned above, we proposed that the strain M15T represented a novel species of the genus Rhizobium, named Rhizobium oryzihabitans sp. nov. The type strain is M15T (=JCM 32903T = ACCC 60121T), and the strain M15T can be a novel biofertilizer Rhizobium to reduce the use of synthetic fertilizers for plant growth promotion.

Diversity and Taxonomic Distribution of Endophytic Bacterial Community in the Rice Plant and Its Prospective

“…Many researchers isolated Bacillus , Pantoea , Methylobacterium and Sphingomonas genera, they are in high abundance with diverse species from the seed [ 23 , 24 ], root [ 25 , 26 ], and leaf part [ 27 , 28 ] of the rice plant ( Supplementary Materials Data 1, Figure S1 ). Most species of Rhizobium , Azospirillum , Burkholderia, and Herbaspirillum were isolated from root tissues with distinct species [ 29 , 30 , 31 , 32 ], and Xanthomonas , Flavobacterium , and Knoellia genera were isolated from seeds ( Supplementary Materials Data 1, Figure S1 ) [ 33 , 34 ]. These endophytes genera also have been identified after isolation from different plants, such as ben tree, ( Moringa peregrina ) [ 35 ], maize ( Zea mays ) [ 36 , 37 ], Datura metel (local name Devil’s Trumpet) [ 38 ], Kudouzi ( Sophora alopecuroides ) [ 39 ], Scots pine ( Pinus sylvestris ) [ 40 ], strawberry ( Fragaria ananassa ) [ 41 , 42 ], wheat ( Triticum aestivum L.) [ 43 ], rose gum ( Eucalyptus grandis ) [ 44 ], sugarcane ( Saccharum officinarum ) [ 45 ], grapevine ( Vitis vinifera ) [ 46 , 47 ], poplar ( Populus deltoides ) [ 48 ], pepper ( Capsicum annuum ) [ 49 ], Huang-Qin ( Scutellaria baicalensis Georgi) [ 50 ], cotton ( Gossypium hirsutum ) [ 51 ], potato ( Solanum tuberosum ) [ 52 ], cucumber ( Cucumis sativus ) [ 53 ], tobacco ( Nicotiana tabacum L.) [ 54 ], peanut ( Echinopsis chamaecereus “Lutea”) [ 55 ], tulasi ( Ocimum sanctum ) [ 56 ], and pea ( Pisum sativum ...…”

“…In the same way, seeds can also be harbored by endophytic bacteria that might be hereditary to new generations. Non-pathogenic bacteria have been categorized, from seeds and roots, parts of rice [ 25 , 29 ], maize [ 37 ], wheat [ 71 ], and other plants [ 37 , 72 , 73 ]. Many endophytes responsible for plant-growth-promoting traits (such as IAA, ACC, siderophore production, nitrogen fixation, phosphorus production, zinc solubilization, and ammonia production) have been isolated from leaves, seeds, stems, and roots of rice plants ( Figure 1 ).…”

“…There are five famously known types of phytohormones, abscisic acid (ABA), auxin, gibberellins (GAs), cytokinins (CKs), ethylene (ET) and Indole-3-acetic acid (IAA), these two hormones (IAA and ET) are the most important participants in building plant–bacterial interactions [ 139 ]. During the last decade, several rice endophytic bacteria showed that they have the great potential for phytohormone production [ 29 , 140 ].…”

“…The most common genera of such bacteria are Alicaligenes faecalis , Azospirillim , Pseudomonas , Xanthomonas , Enterbacter cloacae , Bradyrhizobium japonicum , and Bacillales ; they have displayed auxin production potential and enhance plant growth [ 143 , 144 ]. Various rice endophytic bacteria have been isolated from stem, roots, and leave tissues of different rice genotypes and have the potential to produce IAA in different amount of concentrations (see Figure 1 ) [ 29 , 59 , 140 , 145 ]. IAA biosynthesis is not the only way in which endophytic bacteria can enhance the growth of host plants.…”

Isolation and Identification of Soil Bacteria from Extreme Environments of Chile and Their Plant Beneficial Characteristics

“…Other mechanisms in which PGP bacteria also participate is in nitrogen fixation, phosphate solubilization, or siderophore production, all of which relate to the increase in nutrient availability in the soil [ 19 ]. Research has been carried out based on the use of PGP in agriculture to improve the yield of fruit trees, vegetables, and cereals [ 20 ] such as potato [ 21 ], wheat [ 22 ], soybean [ 23 ], apple [ 24 ], and tomato [ 25 ], among others [ 26 , 27 ]. However, the isolation and application of PGP from extreme conditions represents a rather unexplored scenario [ 28 ].…”