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Journal of Arid Land  2020, Vol. 12 Issue (5): 730-740    DOI: 10.1007/s40333-020-0019-4
Research article     
Endophytic bacteria associated with halophyte Seidlitzia rosmarinus Ehrenb. ex Boiss. from saline soil of Uzbekistan and their plant beneficial traits
Vyacheslav SHURIGIN1,*(), Dilfuza EGAMBERDIEVA2,3, LI Li2, Kakhramon DAVRANOV4, Hovik PANOSYAN5, Nils-Kåre BIRKELAND6, Stephan WIRTH3, Sonoko D BELLINGRATH-KIMURA3,7
1Faculty of Biology, National University of Uzbekistan, Tashkent 100174, Uzbekistan
2Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
3Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg 15374, Germany
4Institute of Microbiology of the Academy of Sciences of the Republic of Uzbekistan, Tashkent 100128, Uzbekistan
5Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Yerevan 0025, Armenia
6Department of Biological Sciences, University of Bergen, NO-5020 Bergen 7803, Norway
7Faculty of Life Science, Humboldt University of Berlin, Berlin 14195, Germany
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Endophytic bacteria of halophytic plants play essential roles in salt stress tolerance. Therefore, an understanding of the true nature of plant-microbe interactions under extreme conditions is essential. The current study aimed to identify cultivable endophytic bacteria associated with the roots and shoots of Seidlitzia rosmarinus Ehrenb. ex Boiss. grown in the salt-affected soil in Uzbekistan and to evaluate their plant beneficial traits related to plant growth stimulation and stress tolerance. Bacteria were isolated from the roots and the shoots of S. rosmarinus using culture-dependent techniques and identified by the 16S rRNA gene. RFLP (Restriction Fragment Length Polymorphism) analysis was conducted to eliminate similar isolates. Results showed that the isolates from the roots of S. rosmarinus belonged to the genera Rothia, Kocuria, Pseudomonas, Staphylococcus, Paenibacillus and Brevibacterium. The bacterial isolates from the shoots of S. rosmarinus belonged to the genera Staphylococcus, Rothia, Stenotrophomonas, Brevibacterium, Halomonas, Planococcus, Planomicrobium and Pseudomonas, which differed from those of the roots. Notably, Staphylococcus, Rothia and Brevibacterium were detected in both roots and shoots, indicating possible migration of some species from roots to shoots. The root-associated bacteria showed higher levels of IAA (indole-3-acetic acid) synthesis compared with those isolated from the shoots, as well as the higher production of ACC (1-aminocyclopropane-1-carboxylate) deaminase. Our findings suggest that halophytic plants are valuable sources for the selection of microbes with a potential to improve plant fitness under saline soils.

Key wordsendophytic bacteria      phylogenetic analysis      halophyte      auxin      plant beneficial traits     
Received: 26 February 2020      Published: 10 September 2020
Corresponding Authors:
About author: *Corresponding author: Vyacheslav SHURIGIN (E-mail:
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Vyacheslav SHURIGIN, Dilfuza EGAMBERDIEVA, LI Li, Kakhramon DAVRANOV, Hovik PANOSYAN, Nils-Kåre BIRKELAND, Stephan WIRTH, Sonoko D BELLINGRATH-KIMURA. Endophytic bacteria associated with halophyte Seidlitzia rosmarinus Ehrenb. ex Boiss. from saline soil of Uzbekistan and their plant beneficial traits. Journal of Arid Land, 2020, 12(5): 730-740.

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Fig. 1 Seidlitzia rosmarinus growing on saline soil in the Surkhandarya Province, Uzbekistan
Isolated strain sequence Closest match among bacteria (16S rRNA gene)
Strain Length (bp) Accession
Species Accession number Identity (%)
JRT1 1452 MH311985 Rothia terrae NR_043968 99.1
JRT2 1450 MH311986 Kocuria palustris NR_026451 98.9
JRT3 1452 MH311987 Pseudomonas baetica NR_116899 98.9
JRT4 1450 MH311988 Staphylococcus warneri NR_025922 99.1
JRT5 1471 MH311989 Staphylococcus epidermidis NR_113957 99.1
JRT6 1460 MH311990 Paenibacillus amylolyticus NR_025882 98.7
JRT7 1466 MH311991 Brevibacterium frigoritolerans NR_115064 99.6
Table 1 Sequence similarities of endophytic bacteria isolated from the roots of Seidlitzia rosmarinus with sequences registered in GenBank
Isolated strain sequence Closest match among bacteria (16S rRNA gene)
Strain Length (bp) Accession
Species Accession number Identity (%)
JST1 1474 MH311992 Staphylococcus warneri NR_025922 99.6
JST2 1445 MH311993 Rothia terrae NR_043968 98.7
JST3 1467 MH311994 Stenotrophomonas pavanii NR_118008 98.4
JST4 1474 MH311995 Staphylococcus succinus NR_028667 98.6
JST5 1471 MH311996 Brevibacterium frigoritolerans NR_115064 99.4
JST6 1458 MH311997 Staphylococcus epidermidis NR_113957 99.4
JST7 1442 MH311998 Halomonas sulfidaeris NR_027185 98.8
JST8 1478 MH311999 Planococcus salinarum NR_116802 98.7
JST9 1471 MH312000 Planomicrobium koreense NR_025011 98.5
JST10 1476 MH312001 Planococcus halocryophilus NR_118149 98.9
JST11 1454 MH312002 Planomicrobium soli NR_134133 98.5
JST12 1464 MH312003 Pseudomonas fluorescens NR_115715 98.6
Table 2 Sequence similarities of endophytic bacteria isolated from the shoots of Seidlitzia rosmarinus with sequences registered in GenBank
Fig. 2 Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences isolated from endophytic bacteria of Seidlitzia rosmarinus, showing the relationship of isolated strains to their closest relatives in GenBank. All presented strains were divided into three groups: Firmicutes, Actinobacteria and Proteobacteria.

Isolated strain
IAA production
Plant growth stimulation (cm) Seed germination percentage (%)
Tr- Tr+ Roots Shoots
R. terrae JRT1 8.4±0.7 11.7±1.0 + 5.2±0.5* 5.4±0.5 89±4
K. palustris JRT2 8.9±0.7 12.5±0.8 + 5.4±0.6* 5.5±0.6 90±6
P. baetica JRT3 10.1±0.8 14.9±1.0 + 5.5±0.5* 5.5±0.6 92±5
S. warneri JRT4 3.8±0.4 4.0±0.4 - 4.7±0.5 4.8±0.5 82±5
S. epidermidis JRT5 4.8±0.5 8.9±0.5 - 4.9±0.5 5.1±0.5 85±5
P. amylolyticus JRT6 11.4±0.9 15.8±1.1 + 5.4±0.6* 5.5±0.5 91±6
B. frigoritolerans JRT7 0.0 0.0 + 4.8±0.5 5.1±0.5 85±6
S. warneri JST1 0.0 0.8±0.4 - 4.6±0.4 5.0±0.5 85±5
R. terrae JST2 8.4±0.7 11.7±1.0 + 5.2±0.5* 5.4±0.5 89±5
S. pavanii JST3 9.5±0.7 20.5±0.9 + 5.5±0.6* 5.6±0.6* 93±4
S. succinus JST4 7.1±0.6 10.9±0.9 - 5.1±0.5 5.3±0.5 87±6
B. frigoritolerans JST5 0.0 0.0 + 4.9±0.5 5.2±0.4 85±5
S. epidermidis JST6 3.3±0.5 6.5±0.5 - 4.7±0.4 5.1±0.5 85±4
H. sulfidaeris JST7 0.0 1.7±0.8 + 4.9±0.5 5.1±0.4 85±4
P. salinarum JST8 0.0 0.0 - 4.6±0.5 4.9±0.4 83±5
P. koreense JST9 7.8±0.7 9.9±0.9 + 5.1±0.6 5.3±0.6 88±6
P. halocryophilus JST10 0.0 1.0±0.4 - 4.7±0.4 5.0±0.5 85±5
P. soli JST11 9.3±0.7 12.3±0.8 + 5.4±0.5* 5.4±0.5 90±6
P. fluorescens JST12 7.2±1.3 11.6±1.5 + 5.6±0.6* 5.7±0.6* 94±4
Control 4.8±0.5 5.1±0.5 85±5
Table 3 Production of IAA (indole-3-acetic acid) and ACC (1-aminocyclopropane-1-carboxylate) deaminase activities in endophytic isolates of Seidlitzia rosmarinus and plant growth promoting abilities
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