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
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.
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.
Fig. 1Seidlitzia rosmarinus growing on saline soil in the Surkhandarya Province, Uzbekistan
Isolated strain sequence
Closest match among bacteria (16S rRNA gene)
Strain
Length (bp)
Accession number
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 number
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 (μg/mL)
ACC deaminase
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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