Microbially Mediated Plant Salt Tolerance and Microbiome based Solutions for Saline Agriculture

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1 Microbially Mediated Plant Salt Tolerance and Microbiome based Solutions for Saline Agriculture

2 Contents Introduction Abiotic Tolerance Approaches Reasons for failure Roots, microorganisms and soil-interaction networks Rhizosphere microbiome and its structure How do microbes help plants tolerate salt stress? Induced systemic tolerance (IST) Tool to study the functional traits of microbial communities Shotgun Metagenomic DNAsequencing Steps of Metagenomic sequencing Conclusion

3 Introduction Climate change-induced soil salinization is a constant threat to agriculture and ecology worldwide. Plants have readily evolved an array of genetic and epigenetic regulatory systems to respond to abiotic stresses such as salinity and drought

4 Abiotic Tolerance Approaches The integration of conventional plant breeding and molecular techniques has increase crop abiotic tolerance. Transgenic plants over expressing a wide range of genes adapt well to high salt environments under laboratory and greenhouse conditions. In general, however, such approaches have not been very successful at increasing tolerance or yield, although they are still being actively pursued.

6 Reasons for failure There are several reasons for this failure. These approaches are: both time-consuming and labor-intensive frequently result in unstable mutants due to the simultaneous manipulation of numerous genes involved in abiotic stress responses. it is still uncertain whether transgenic crops will become generally publicly acceptable.

Roots, microorganisms and soil-interaction networks plant roots growing in soil are in contact with highly diverse microbes The below ground ecological interaction network

7 Roots, microorganisms and soil-interaction networks plant roots growing in soil are in contact with highly diverse microbes The below ground ecological interaction network between the root, soil and microorganisms plays a crucial role in supporting normal growth and defending against unsuitable conditions for both the host and its associated organisms.

8 Cont.. Some important mutualistic microorganisms can reduce the incidence of plant diseases, promote nutrient utilization, and enhance a plant s ability to resist abiotic stress. Soil salinity is a major factor among abiotic stresses. It may be due to natural consequences or may be due to human impacts like intensive irrigations. Approximately % of the irrigated lands have been severely damaged by salinity.

9 Rhizosphere microbiome and its structure There are four continuous root-soil compartments (bulk soil, rhizosphere, rhizoplane and endosphere) that each sustains distinctive microbial communities Root exudates likely influence on the rhizosphere microbiome. With regards to the rhizoplane, owing to direct contact with root surfaces and exposure to root exudates, yet another refinement of community structure may occur in this microenvironment, in which bacterial adhesion and biofilm formation frequently take place.

10 How do microbes help plants tolerate salt stress?

11 When there is stress.. Plants when subjected to salinity, drought, and pathogen stresses are known to produce excessive ethylene, which severely retard root development. Thus, plants with reduced ethylene levels would finally overcome salt-induced growth inhibition. ACC deaminase, catalyzes the conversion of ACC (the precursor of ethylene biosynthesis) to ammonia and α- ketobutyrate. Considerable attention has been paid to the isolation of ACC deaminase producing microbes for their utilization in direct plant growth promotion under saline environments

12 Rhizospheric and endophytic bacteria as helpers for alleviating plant salt stress Any community of root-associated microorganisms is dominated by plant-growth-promoting rhizobacteria(pgpr) and endophytic bacteria. One of the most striking functions of PGPR is that they show the ability to produce ACC deaminase. In one study the ethylene content in tomato seedlings exposed to high salt was reduced by application PGPR(Bacillus subtilis GB03) indicating that bacterial ACC deaminase was functional.

14 Induced systemic tolerance (IST) Some PGPR also elicit physical or chemical changes related to plant defense, a process referred to as induced systemic tolerance (IST). It seems that multiple bacterial determinants are involved in IST, including phosphate solubilization, 1-aminocyclopropane-1- carboxylic acid (ACC)-deaminase activity, and the production of volatiles, indole-3-acetic acid (IAA), and exopolysaccharides

15 Cont.. Among the 600 Arabidopsis genes isolated by transcriptome analysis, transcriptional expression of HIGH-AFFINITY K + TRANSPORTER 1 (HKT1), which controls Na + import in roots, was decreased. HKT1 has been shown to adjust Na + and K + levels differentially, depending on the plant tissue.

17 Cont.. Transcriptional validation revealed that bacterial VOCs down regulated HKT1 expression in roots, but unregulated it in shoot tissues, thereby orchestrating lower Na + levels in the whole plant. Overall, plant perception of bacterial VOC causes a tissue-specific regulation of HKT1 that controls Na+ homeostasis under salt stress.

18 Tool to study the functional traits of microbial communities The isolation of microbes in pure culture is necessary to study them in detail, screen for specific traits and determine the genetic components behind these beneficial phenotypes directly. There is need of determining the cultivation-unbiased structure of the community and the functional traits of its all members

19 Shotgun Metagenomic DNAsequencing This approach will answer the question that which microbial genes are enriched in a specific microhabitat. Metatranscriptomics is employed to identify transcript abundances and link gene function with specific conditions.

20 Shotgun Metagenomic DNAsequencing Shotgun metagenomic DNA sequencing is a relatively new and powerful environmental sequencing approach that provides insight into community biodiversity and function. It allow researchers to determine which microbes are present in the community and what they might be doing.

21 Steps of Metagenomic sequencing 1. Quantification of its taxonomic diversity Taxonomic diversity serves as a way of profiling a community and can be used to ascertain the similarity of two or more communities. It may provide some insight into the biological function of the community when it contains members of functionally described taxa.

23 Marker Gene Analysis 2. There are two general methods by which marker genes are used to taxonomically annotate metagenomes. The first relies on sequence similarity between the read and the marker genes. The second approach uses phylogenetic information, which may take longer to calculate, but may also provide greater accuracy.

24 Limitations First, this strategy operates under the assumption that the relatively small fraction of the metagenome that is homologous to marker genes represents an accurate sampling of the entire taxonomic distribution of the community. Second, marker gene analysis is not appropriate for taxa that do not contain the markers being explored. Thanks to recent efforts to identify phylogenetic clade-specific marker genes Expanding the phylogenetic diversity of available genomes sequences can mitigate these limitations.

25 What Are They Capable Of Doing? Inferring Biological Function The functional diversity of a community can be quantified by annotating metagenomic sequences with functions. This usually involve identifying metagenomic reads that contain protein coding sequences and comparing the coding sequence to a database of genes, proteins, protein families, or metabolic pathways for which some functional information is known.

26 GENE PREDICTION 3. Gene prediction determines which metagenomic reads contain coding sequences. Sequence Alignment The alignments can then be analyzed to identify those sequences that encode translated peptides that exhibit homology to proteins in the database. This can be conducted by using sequence translation tools like transeq to translate reads using blastp or fast blast algorithms like USEARCH, RAPsearch or lastp.

27 Cont.. De novo gene prediction, on the other hand, can potentially identify novel genes. Here, gene prediction models, which are trained by evaluating various properties of microbial genes are used to assess whether a metagenomic read contains a gene and does not rely on sequence similarity to a referenced at a base to do so. As a result, these methods can identify genes in the metagenome that share common properties with other microbial genes but that may be highly diverged from any gene that has been discovered to date. There are several tools that can be used for de novo gene prediction, including Meta Gene Glimmer-MG, MetaGeneMark, FragGeneScan, Orphelia, and MetaGun.

28 Findings-end step Once the metagenomic sequence has been compared to all proteins or all models, it can either be classified into (1) a single family (e.g., the family with the best hit), (2) a series of families (e.g., all families that exhibit a significant classification score), or (3) no family, which suggests that the protein may be novel, highly diverged, or spurious.

29 Conclusion From an ecological perspective, the plant microbiome is considered a second plant genome (also called the pan-genome) with the capacity to enhance host stress tolerance. Comparing metagenomic reads to a database of sequences tends to be relatively fast and may produce more specific hits for reads that are closely related to sequences in the database. Knowing which analyses to conduct and which tools to apply remain confusing questions for many scientists. The answer depends largely on several variables, including the hypothesis and goals, the experimental design, and the known properties of the community.

Role of PGPR in sustainable agriculture: Global climate Change and Water sustainability

Role of PGPR in sustainable agriculture: Global climate Change and Water sustainability 4 th Asian PGPR Conference, Hanoi 3-6 th May, 2015 Rupak Kumar Sarma Life Science Division Institute of Advanced