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Molecular Characterization of Microsymbionts Associated with Root Nodules of Crotalaria Burhia Buch.-Ham

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Molecular Characterization of Microsymbionts Associated with Root Nodules of Crotalaria Burhia Buch.-Ham Indian Journal of Experimental Biology Vol. 56, June 2018, pp. 373-384 Molecular characterization of microsymbionts associated with root nodules of Crotalaria burhia Buch.-Ham. ex Benth., a native keystone legume species from Thar Desert of India Indu Singh Sankhla1,2, Raju Ram Meghwal1, Sunil Choudhary1,3, Sonam Rathi1, Nisha Tak1, Alkesh Tak1 & Hukam Singh Gehlot1* 1BNF and Microbial Genomics Laboratory, Department of Botany, Jai Narain Vyas University, Jodhpur-342 033, Rajasthan, India 2Department of Botany, University of Rajasthan, Jaipur-302 004, Rajasthan, India 3ICFRE-Arid Forest Research Institute (AFRI), Jodhpur-302 005, Rajasthan, India Received 19 April 2016; revised 14 July 2017 Establishment of legume-rhizobia symbiosis has ample agronomic and ecological significance. Characterization of native rhizobia could enhance our understanding of their natural distribution and co-evolution. The Great Indian Thar Desert is an ecologically significant unique habitat with its flora and fauna. Crotalaria spp. is an economically important legume widely distributed in the Thar Desert and can be considered its one of the bioresources, particularly for biological nitrogen fixation with their symbiotic rhizobia. Here, we examined the legume Crotalaria burhia Buch.-Ham. ex Benth. in search of potential novel rhizobial species. Out of 72 root nodule bacterial (RNB) strains isolated from C. burhia, 51 rhizobia-like strains were examined for genetic diversity based on ARDRA and RAPD patterns. BLASTn sequence similarity results based on 16S rRNA gene of selective thirteen strains representing four ARDRA types revealed that they were related to genera Ensifer, Rhizobium and Bradyrhizobium. In 16S rRNA gene phylogeny, five (CB5, CB17, CB36, CB44, CB56) strains were closer to Ensifer kostiensis, three (CB6, CB12, CB32) to E. terangae and CB11 showed similarity with E. kostiensis and E. saheli. Strain CB4 was similar to Bradyrhizobium yuanmingense and three (CB29, CB31, CB46) strains were closer to species of Rhizobium (R. etli, R. sullae and R. borbori respectively). Symbiotic (nodA and nifH) genes phylogeny of Ensifer sp. CB56 was incongruent and showed close similarity with E. fredii whereas sym gene phylogeny of Bradyrhizobium sp. CB4 was congruent with 16S rRNA gene phylogeny. In Rhizobium strains sym genes could not be amplified and they failed to nodulate host. Our study suggests that C. burhia is nodulated by diverse strains of Ensifer and Bradyrhizobium in alkaline soil of Thar Desert and these strains effectively cross-nodulated crop Vigna radiata. Keywords: ARDRA, Bradyrhizobium, Burhia Rattlepod, Ensifer, nifH, Nitrogen fixation, nodA, Nodulation, Root nodule bacterial (RNB) strains Legume-rhizobia symbiosis known for biological The genus Crotalaria L. is the third largest in nitrogen fixation have long term agronomical and Papilionoideae subfamily of Leguminosae having ecological significance and is one of the alternative to more than 700 species3. It is distributed in tropical and nitrogen fertilizers. Rhizobia are Gram negative, sub-tropical regions of the world with the majority of aerobic, soil bacteria with ability to mostly form N species (543) native to tropical Africa and fixing nodules on roots of legumes1. Most of the Madagascar. In India, it is the largest legume taxa legume-rhizobia symbiosis studies have been carried comprising 93 species of which 27 are endemic4. out on either agricultural crops (soybean, mungbean, Many species of Crotalaria have great economic pea and chickpea) or pasture legumes (clover and importance in terms of insecticides, fibres, silage and alfalfa). From last two decades such studies have been green manure having agronomic values4,5. Crotalaria extended to wild/native legumes from tropical and burhia Buch.-Ham. ex Benth., (Burhia Rattlepod) semi-tropical climatic zones that resulted in locally called ‘Shinio’, is a perennial bushy legume discovering several novel species and genera belonging widely distributed on sandy areas throughout the Thar to class alphaproteobacteria and betaproteobacteria2. Desert of India and adjoining Pakistan. The Indian ________ Thar Desert is characterized by erratic precipitation, *Correspondence: high irradiation, high temperature and saline tracts6. Phone: +91 94141 24939 (Mob.) E-mail: [email protected] Overall, the area is alkaline and the soil has been 374 INDIAN J EXP BIOL, JUNE 2018 classified as ‘desert soil’ poor in nitrogen and available Methylobacterium nodulans21. Furthermore, Liu et al.22 phosphorus. Therefore the plants, animals, and microbes isolated Rhizobium and Bradyrhizobium strains from growing in Thar Desert are continuously under biotic nodules of C. pallida in China, while Rocha23 isolated and abiotic stresses. Gehlot et al.7 suggested some Mesorhizobium sp. from root nodules of traditional and modern scientific approaches for C. spectabilis. On the basis of Amplified r-DNA characterization, conservation and sustainable utilization Restriction Analysis (ARDRA) Singha et al.24 identified of bioresources of the Thar Desert. Nodulation in three groups of rhizobial strains (Rhizobium, number of wild/native legumes of Thar Desert have Bradyrhizobium and Mesorhizobium) from C. pallida in been reported as well as root nodule microsymbionts of Assam, India. Sankhla et al.12 reported that several legumes have been characterized at molecular C. medicagenia is nodulated by Ensifer strains in sandy and genomic level recently8-19. areas of Indian Thar Desert. In this study, we The C. burhia is one of the keystone species of investigated genetic diversity of root nodule bacteria Thar Desert and has a great potential in terms of (RNB) associated with C. burhia and characterized its restoration of soil fertility through nitrogen fixation rhizobia at molecular level including symbiotic genes. and also in prevention of desertification through its soil binding and sand dune stabilizing properties, Materials and Methods hence it have great ecological importance. Nodule sampling and isolation of rhizobia Crotalaria has been reported to be nodulating by Root nodules of C. burhia were collected from 25 Bradyrhizobium strains20. However, Crotalaria sites in five districts of Western Rajasthan (Table 1). podocarpa is nodulated by a novel rhizobia The nodules were collected during the monsoon and Table 1 — Nodulation status of Crotalaria burhia growing at different sampling sites throughout Thar Desert and origin of root nodule bacterial (RNB) strains District Soil sampling site Geographical coordinates pH OC Total N P Avg. no. of Purified root nodule (%) (%) (kg/ha) nodules per plant bacterial strains Jodhpur Amritlal stadium 26°20'25.40"N/73° 3'3.09"E 8.2 0.16 0.0078 9.2 08 CB1, CB2, CB45, CB46r, CB47, CB48 JNVU New 26°14'49.85"N/73° 8.2 0.18 0.0091 12.4 09 CB5e, CB7, CB27, CB28, Campus 1'18.65"E CB29r, CB30 Kailana 26°18'5.83"N/72°58'29.38"E 8.2 0.10 0.0052 8.2 09 CB8, CB55 Osian 26°44'26.57"N/72°53'49.26"E 8.9 0.14 0.0071 18.4 14 CB38, CB39, CB40, CB42, CB44e Pratapnagar 26°17'29.28"N/73° 0'6.36"E 8.8 0.23 0.0048 16.3 09 CB49, CB50, CB51 Shergarh 26°19'10.58"N/72°18'1.42"E 8.7 0.19 0.0112 9.2 09 CB67, CB68 Nagaur Alai 27°19'24.91"N/73°35'6.99"E 8.2 0.24 0.0092 6.4 08 CB10, CB61 Baghnada 27° 8'42.94"N/73°48'32.42"E 8.2 0.26 0.0111 11.2 11 CB6e, CB15, CB16 Deh 27°18'30.40"N/73°54'53.51"E 8.4 0.28 0.0069 8.2 10 CB3, CB4b Harima 27°15'26.84"N/73°51'39.74"E 8.5 0.29 0.0071 7.8 14 CB21, CB22, CB23 Inana 27° 8'2.63"N/73°49'39.20"E 8.1 0.22 0.0114 10.8 12 CB18, CB19, CB20 Tausar 27° 6'36.85"N/73°46'30.60"E 8.4 0.23 0.0121 9.8 10 CB24, CB25, CB26 Barmer Barmer 25°45'10.09"N/71°26'5.31"E 8.2 0.14 0.0079 10.2 08 CB33, CB43 Bhuka 25°39'54.66"N/72° 0'54.03"E 8.8 0.13 0.0095 9.2 09 CB31r, CB32e, CB34 Chohtan 25°29'44.82"N/71° 5'6.90"E 8.1 0.16 0.0048 11.2 05 CB35, CB36e, CB37 Nimdee 26° 4'2.97"N/71°19'48.46"E 8.6 0.18 0.0081 11.9 07 CB9, CB11e, CB12e Jaisalmer Chandhan 26°59'18.13"N/71°18'13.62"E 8.8 0.17 0.0117 6.4 07 CB52, CB41 Jaisalmer 26°53'49.55"N/70°56'31.18"E 8.3 0.19 0.0050 6.9 07 CB63, CB64 Kuldhera 26°52'28.36"N/70°46'34.28"E 8.6 0.19 0.0094 5.5 09 CB56e, CB57 Longewala 27°30'8.57"N/70° 7'28.76"E 8.5 0.29 0.0098 7.1 07 CB65, CB66 Pokaran 26°58'25.49"N/71°54'6.92"E 8.7 0.22 0.0069 5.1 05 CB71, CB72 Sum 26°50'31.14"N/70°32'53.19"E 8.1 0.11 0.0069 8.7 09 CB58, CB62, CB69, CB70 Bikaner Bikaner 28° 1'49.04"N/73°15'30.63"E 7.9 0.21 0.0047 10.2 09 CB53, CB54 Deshnok 27°47'20.09"N/73°20'22.46"E 8.7 0.21 0.0117 11.9 10 CB13, CB14, CB17e Nokha 27°34'11.22"N/73°27'36.13"E 9.0 0.29 0.0092 11.2 08 CB59, CB60 [CB, Crotalaria burhia; Strains identified as eEnsifer sp., bBradyrhizobium sp. and rRhizobium sp. on the basis of 16S rRNA gene sequences] Sankhla et al.: CHARACTERIZATION OF MICROSYMBIONTS ASSOCIATED WITH CROTALARIA ROOT NODULES 375 post-monsoon season (July-October) in the years of Taq DNA polymerase, 1.2 μM of each of the 6 2011, 2012 and 2013.
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