Multilocus Sequence Analysis of Root Nodule Bacteria Associated with <i>Lupinus</i> spp. and <i>Glycine max</i>

Abstract

Lupinus is known to form endophytic associations with both nodulating and non-nodulating bacteria. In this study, multilocus sequence analysis (MLSA) was used to analyze phylogenetic relationships among root nodule bacteria associated with Lupinus and soybean. Out of 17bacterial strains analyzed, 13 strains isolated from root nodules of Lupinus spp. were obtained from the National Rhizobium Germplasm Resource Collection, USDA. Additionally, two strains of root-nodule bacteria isolated each from native Lupinus and domestic soybean were examined. Sequences of the 16S rRNA gene and three housekeeping genes (atpD, dnaK and glnII) were used. All the reference genes were retrieved from the existing complete genome sequences only. The clustering of 12 of the strains was consistent among single and concatenated gene trees, but not USDA strains 3044, 3048, 3504, 3715, and 3060. According to the concatenated phylogeny, we suggest that USDA 3040, 3042, 3044, 3048, 3051, 3060, 3504, 3709 and 3715 are Bradyrhizobium, USDA 3063 and 3717 are Mesorhizobium, USDA 3043 is Burkholderia and USDA 3057a is Microvirga. The two strains isolated from native lupines in this study are Burkholderia and Rhizobium, whereas the two from domestic soybean are Bradyrhizobium. This study emphasizes the robustness of MLSA, the diversity of bacterial species that are capable of nodulating lupine and the substantial capability of Burkholderia spp. to colonize lupine root nodules.

Microvirgasp. symbiovar mediterranense nodulatesLupinus cosentiniigrown wild in Morocco

“…), Burkholderia (Beligala et al . ), Allorhizobium , Mesorhizobium, Rhizobium and Sinorhizobium (Pudełko ; El Hilali et al . ), can be found within lupine nodules.…”

“…, ), L. subcarnosus (Beligala et al . ) and L. angustifolius (Rejili et al . ) emphasize the capability of Microvirga to colonize lupine root nodules.…”

“…, ) and L. subcarnosus (Beligala et al . ) and Burkholderia have been isolated from the later plant species.…”

“…Lupinus species have been shown to be nodulated by slow-growing rhizobia of the genus Bradyrhizobium, including B. japonicum, B. lupini, B. canariense, B. diazoefficiens and B. elkanii species (Peix et al 2015;Shamseldin et al 2017;Vel azquez et al 2017;Ste z pkowski et al 2018;Mellal et al 2019). Also, fast-growing strains of the species Ochrobactrum lupini isolated from Lotus honoratus (Trujillo et al 2005), of the genus Microvirga from L. texensis (Ardley et al 2012), L. micranthus (Msaddak et al 2017a(Msaddak et al , 2017b and L. subcarnosus (Beligala et al 2017) and Burkholderia have been isolated from the later plant species.…”

Phylogeny and Phylogeography of Rhizobial Symbionts Nodulating Legumes of the Tribe Genisteae

“…It seems, however, that M. loti is not the only Mesorhizobium species that is involved in root-nodule symbiosis with Genisteae. Recently, two Mesorhizobium strains isolated from North American lupins, one from Lupinus densiflorus, and the other from L. succulentus , were shown to have a phylogenetic affinity to Mesorhizobium ciceri —a species that until now has not been implicated in the symbiosis with genistoid legumes [ 157 ]. In the Mediterranean, Mesorhizobium strains nodulate with native Genisteae spp, including Genista saharae , R. raetam , Teline monspessulana , and three lupin species (see Table 1 ).…”