Sphingomonas pokkalii sp. nov., a novel plant associated rhizobacterium isolated from a saline tolerant pokkali rice and its draft genome analysis

Menon, Rahul R.; Kumari, Saroj; Kumar, P. Anil; Verma, Ashish; Krishnamurthi, Srinivasan; Rameshkumar, N.

doi:10.1016/j.syapm.2019.02.003

Cited by 40 publications

(21 citation statements)

References 54 publications

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“…Although Ss and SDY samples displayed similar proportions of Actinobacteria (26:24%), we found that levels were more than three times higher in nodule samples, suggesting that Actinobacteria may be involved in saline tolerance in the rhizosphere of wild soybean grown in coastal regions (Bhatti et al, 2017). In α-proteobacteria, nS samples had more than five times as many Sphingomonas species than nD samples; however, it has previously been reported that these root zones display similar proportions of Sphingomonas species (Menon et al, 2019). Similarly, nS samples also harbored a higher proportion of the γ-proteobacteria Enterobacteriaceae and Pseudomonas families, which have also been reported as PGPR (Agler et al, 2016;Chu et al, 2019).…”

Section: Comparison Of Bacterial Community Composition In Different Scontrasting

confidence: 60%

Nodule and Root Zone Microbiota of Salt-Tolerant Wild Soybean in Coastal Sand and Saline-Alkali Soil

et al. 2020

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Soil salinization limits crop growth and yield in agro-ecosystems worldwide by reducing soil health and altering the structure of microbial communities. Salt-tolerant plant growthpromoting rhizobacteria (PGPR) alleviate plant salinity stress. Wild soybean (Glycine soja Sieb. and Zucc.) is unique in agricultural ecosystems owing to its ability to grow in salinealkali soils and fix atmospheric nitrogen via symbiotic interactions with diverse soil microbes. However, this rhizosphere microbiome and the nodule endosymbionts have not been investigated to identify PGPR. In this study, we investigated the structural and functional rhizosphere microbial communities in saline-alkali soil from the Yellow River Delta and coastal soil in China, as well as wild soybean root nodule endosymbionts. To reveal the composition of the microbial ecosystem, we performed 16S rRNA and nifH gene amplicon sequencing on root nodules and root zones under different environmental conditions. In addition, we used culture-independent methods to examine the root bacterial microbiome of wild soybean. For functional characterization of individual members of the microbiome and their impact on plant growth, we inoculated isolates from the root microbiome with wild soybean and observed nodulation. Sinorhizobium/Ensifer accounted for 97% of the root nodule microbiome, with other enriched members belonging to the phyla Actinobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, and Gemmatimonadetes; the genera Sphingomonas, Microbacterium, Arthrobacter, Nocardioides, Streptomyces, Flavobacterium, Flavisolibacter, and Pseudomonas; and the family Enterobacteriaceae. Compared to saline-alkali soil from the Yellow River Delta, coastal soil was highly enriched for soybean nodules and displayed significant differences in the abundance and diversity of β-proteobacteria, δ-proteobacteria, Actinobacteria, and Bacteroidetes. Overall, the wild soybean root nodule microbiome was dominated by nutrient-providing Sinorhizobium/ Ensifer and was enriched for bacterial genera that may provide salt resistance. Thus, this reductionist experimental approach provides an avenue for future systematic and functional studies of the plant root microbiome.

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Section: Comparison Of Bacterial Community Composition In Different Scontrasting

confidence: 60%

Nodule and Root Zone Microbiota of Salt-Tolerant Wild Soybean in Coastal Sand and Saline-Alkali Soil

et al. 2020

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“…Li et al 21 showed that in contrast to the widely grown, but salt-sensitive rice variety IR-29, genes responsible for cell wall integrity, detoxifying ROS and photosynthesis are highly expressed in the salt-tolerant Pokkali rice. Novel rhizosphere-associated bacteria [22][23][24] such as Sphingomonas pokkali 25 have been shown to be associated with adaptation of the Pokkali varieties to the brackish rhizospheric environment. We show that the Pokkali races harbor Figure 3.…”

Section: Discussionmentioning

confidence: 99%

An endophyte from salt-adapted Pokkali rice confers salt-tolerance to a salt-sensitive rice variety and targets a unique pattern of genes in its new host

Sampangi-Ramaiah¹,

Jagadheesh²,

Dey³

et al. 2020

Sci Rep

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Endophytes, both of bacterial and fungal origin, are ubiquitously present in all plants. While their origin and evolution are enigmatic, there is burgeoning literature on their role in promoting growth and stress responses in their hosts. We demonstrate that a salt-tolerant endophyte isolated from salt-adapted Pokkali rice, a Fusarium sp., colonizes the salt-sensitive rice variety IR-64, promotes its growth under salt stress and confers salinity stress tolerance to its host. Physiological parameters, such as assimilation rate and chlorophyll stability index were higher in the colonized plants. Comparative transcriptome analysis revealed 1348 up-regulated and 1078 down-regulated genes in plants colonized by the endophyte. Analysis of the regulated genes by MapMan and interaction network programs showed that they are involved in both abiotic and biotic stress tolerance, and code for proteins involved in signal perception (leucine-rich repeat proteins, receptor-like kinases) and transduction (ca 2+ and calmodulin-binding proteins), transcription factors, secondary metabolism and oxidative stress scavenging. For nine genes, the data were validated by qPCR analysis in both roots and shoots. Taken together, these results show that salt-adapted Pokkali rice varieties are powerful sources for the identification of novel endophytes, which can be used to confer salinity tolerance to agriculturally important, but salt-sensitive rice varieties. Salinity stress is one of the most devastating abiotic stresses that affect growth, development and productivity of major crops. A soil is termed saline if its osmotic pressure is approximately 0.2 M Pa with an electrical conductivity of 4 dS/m or more (equivalent to ~40 mM NaCl) 1,2. It is estimated that at least 50% of the arable land worldwide will be salt affected by the year 2050 and this is expected to further increase due to global climate change 3. Rice (Oryza sativa L.), a major staple food crop, is one of the most salt-sensitive cereals 4. In the Indo-Gangetic Basin in India, an estimated 45% loss in rice production was attributed to salinity stress alone 5,6. The responses of plants to salinity stress are often multi-faceted and complex. In the initial phase, salinity stress manifests itself as osmotic stress with reduction in water uptake by plants. This triggers a range of metabolic and molecular cascades such as inhibition of cell expansion, stomatal conductance, photosynthetic activity, abscisic acid (ABA)-mediated responses followed by stimulation of the SOD and peroxidase activities as well as accumulation of osmolytes like proline. The later phase of salinity stress leads to ionic stress, which is due to the

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“…Bacteria of the family Sphingomonadaceae , also just referred to as the sphingomonads, are ubiquitously distributed Alphaproteobacteria. They are found in soil, especially when contaminated with mineral oil hydrocarbons [4], associated with plants [5–7], as well as in marine [8] or freshwater [9] environments. Interestingly, they are also frequently reported to occur in tap water [10] and drinking-water distribution systems [11].…”

Section: Introductionmentioning

confidence: 99%

Genetic and physiological analysis of biofilm formation on different plastic surfaces by Sphingomonas sp. strain S2M10 reveals an essential function of sphingan biosynthesis

et al. 2020

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Alphaproteobacteria belonging to the group of the sphingomonads are frequently found in biofilms colonizing pure-water systems, where they cause technical and hygienic problems. In this study, physiological properties of sphingomonads for biofilm formation on plastic surfaces were analysed. Sphingomonas sp. strain S2M10 was isolated from a used water-filtration membrane and submitted to transposon mutagenesis for isolating mutants with altered biofilm formation. Mutants showing strongly decreased biofilm formation carried transposon insertions in genes for the biosynthesis of the polysaccharide sphingan and for flagellar motility. Flagella-mediated attachment was apparently important for biofilm formation on plastic materials of intermediate hydrophobicity, while a mutant with defect in spnB, encoding the first enzyme in sphingan biosynthesis, showed no biofilm formation on all tested materials. Sphingan-dependent biofilm formation was induced in the presence of specific carbon sources while it was not induced in complex medium with yeast extract and tryptone. The regulation of sphingan-based biofilm formation was investigated by interfering with the CckA/ChpT/CtrA phosphorelay, a central signal-transduction pathway in most Alphaproteobacteria. Construction and ectopic expression of a kinase-deficient histidine kinase CckA caused cell elongation and massive sphingan-dependent cell aggregation. In addition, it caused increased activity of the promotor of spnB. In conclusion, these results indicate that sphingan-based biofilm formation by sphingomonads might be triggered by specific carbon sources under prototrophic conditions resembling a milieu that often prevails in pure-water systems.

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Sphingomonas pokkalii sp. nov., a novel plant associated rhizobacterium isolated from a saline tolerant pokkali rice and its draft genome analysis

Cited by 40 publications

References 54 publications

Nodule and Root Zone Microbiota of Salt-Tolerant Wild Soybean in Coastal Sand and Saline-Alkali Soil

Nodule and Root Zone Microbiota of Salt-Tolerant Wild Soybean in Coastal Sand and Saline-Alkali Soil

An endophyte from salt-adapted Pokkali rice confers salt-tolerance to a salt-sensitive rice variety and targets a unique pattern of genes in its new host

Genetic and physiological analysis of biofilm formation on different plastic surfaces by Sphingomonas sp. strain S2M10 reveals an essential function of sphingan biosynthesis

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