Ratna Prabha

Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies

Abiotic stresses are the foremost limiting factors for agricultural productivity. Crop plants need to cope up adverse external pressure created by environmental and edaphic conditions with their intrinsic biological mechanisms, failing which their growth, development, and productivity suffer. Microorganisms, the most natural inhabitants of diverse environments exhibit enormous metabolic capabilities to mitigate abiotic stresses. Since microbial interactions with plants are an integral part of the living ecosystem, they are believed to be the natural partners that modulate local and systemic mechanisms in plants to offer defense under adverse external conditions. Plant-microbe interactions comprise complex mechanisms within the plant cellular system. Biochemical, molecular and physiological studies are paving the way in understanding the complex but integrated cellular processes. Under the continuous pressure of increasing climatic alterations, it now becomes more imperative to define and interpret plant-microbe relationships in terms of protection against abiotic stresses. At the same time, it also becomes essential to generate deeper insights into the stress-mitigating mechanisms in crop plants for their translation in higher productivity. Multi-omics approaches comprising genomics, transcriptomics, proteomics, metabolomics and phenomics integrate studies on the interaction of plants with microbes and their external environment and generate multi-layered information that can answer what is happening in real-time within the cells. Integration, analysis and decipherization of the big-data can lead to a massive outcome that has significant chance for implementation in the fields. This review summarizes abiotic stresses responses in plants in-terms of biochemical and molecular mechanisms followed by the microbe-mediated stress mitigation phenomenon. We describe the role of multi-omics approaches in generating multi-pronged information to provide a better understanding of plant–microbe interactions that modulate cellular mechanisms in plants under extreme external conditions and help to optimize abiotic stresses. Vigilant amalgamation of these high-throughput approaches supports a higher level of knowledge generation about root-level mechanisms involved in the alleviation of abiotic stresses in organisms.

ChloroMitoSSRDB 2.00: more genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection

Organelle genomes evolve rapidly as compared with nuclear genomes and have been widely used for developing microsatellites or simple sequence repeats (SSRs) markers for delineating phylogenomics. In our previous reports, we have established the largest repository of organelle SSRs, ChloroMitoSSRDB, which provides access to 2161 organelle genomes (1982 mitochondrial and 179 chloroplast genomes) with a total of 5838 perfect chloroplast SSRs, 37 297 imperfect chloroplast SSRs, 5898 perfect mitochondrial SSRs and 50 355 imperfect mitochondrial SSRs across organelle genomes. In the present research, we have updated ChloroMitoSSRDB by systematically analyzing and adding additional 191 chloroplast and 2102 mitochondrial genomes. With the recent update, ChloroMitoSSRDB 2.00 provides access to a total of 4454 organelle genomes displaying a total of 40 653 IMEx Perfect SSRs (11 802 Chloroplast Perfect SSRs and 28 851 Mitochondria Perfect SSRs), 275 981 IMEx Imperfect SSRs (78 972 Chloroplast Imperfect SSRs and 197 009 Mitochondria Imperfect SSRs), 35 250 MISA (MIcroSAtellite identification tool) Perfect SSRs and 3211 MISA Compound SSRs and associated information such as location of the repeats (coding and non-coding), size of repeat, motif and length polymorphism, and primer pairs. Additionally, we have integrated and made available several in silico SSRs mining tools through a unified web-portal for in silico repeat mining for assembled organelle genomes and from next generation sequencing reads. ChloroMitoSSRDB 2.00 allows the end user to perform multiple SSRs searches and easy browsing through the SSRs using two repeat algorithms and provide primer pair information for identified SSRs for evolutionary genomics. Database URL: http://www.mcr.org.in/chloromitossrdb

Synonymous codon usage in Thermosynechococcus elongatus (cyanobacteria) identifies the factors shaping codon usage variation.

Analysis of synonymous codon usage pattern in the genome of a thermophilic cyanobacterium, Thermosynechococcus elongatus BP-1 using multivariate statistical analysis revealed a single major explanatory axis accounting for codon usage variation in the organism. This axis is correlated with the GC content at third base of synonymous codons (GC3s) in correspondence analysis taking T. elongatus genes. A negative correlation was observed between effective number of codons i.e. Nc and GC3s. Results suggested a mutational bias as the major factor in shaping codon usage in this cyanobacterium. In comparison to the lowly expressed genes, highly expressed genes of this organism possess significantly higher proportion of pyrimidine-ending codons suggesting that besides, mutational bias, translational selection also influenced codon usage variation in T. elongatus. Correspondence analysis of relative synonymous codon usage (RSCU) with A, T, G, C at third positions (A3s, T3s, G3s, C3s, respectively) also supported this fact and expression levels of genes and gene length also influenced codon usage. A role of translational accuracy was identified in dictating the codon usage variation of this genome. Results indicated that although mutational bias is the major factor in shaping codon usage in T. elongatus, factors like translational selection, translational accuracy and gene expression level also influenced codon usage variation.

Genome-wide comparative analysis of codon usage bias and codon context patterns among cyanobacterial genomes.

With the increasing accumulation of genomic sequence information of prokaryotes, the study of codon usage bias has gained renewed attention. The purpose of this study was to examine codon selection pattern within and across cyanobacterial species belonging to diverse taxonomic orders and habitats. We performed detailed comparative analysis of cyanobacterial genomes with respect to codon bias. Our analysis reflects that in cyanobacterial genomes, A- and/or T-ending codons were used predominantly in the genes whereas G- and/or C-ending codons were largely avoided. Variation in the codon context usage of cyanobacterial genes corresponded to the clustering of cyanobacteria as per their GC content. Analysis of codon adaptation index (CAI) and synonymous codon usage order (SCUO) revealed that majority of genes are associated with low codon bias. Codon selection pattern in cyanobacterial genomes reflected compositional constraints as major influencing factor. It is also identified that although, mutational constraint may play some role in affecting codon usage bias in cyanobacteria, compositional constraint in terms of genomic GC composition coupled with environmental factors affected codon selection pattern in cyanobacterial genomes.

Microbial Inoculants in Sustainable Agricultural Productivity

Soil health is represented by its continuous capacity to function as a vital living system. Since soil health is the major driving factor for sustainable agriculture, it has to be preserved. Microorganisms are an essential and integral part of living soil infl uencing various biogeochemical cycles on major nutrients such as carbon, nitrogen, sulphur, phosphorous and other minerals and play superior role in maintaining soil health than other biological component of soil. They also have the capacity to suppress soil borne pathogens and indirectly help in agricultural productivity. Besides contribution of specifi c microbes to soil health by participating on nutrient cycles, certain other microbes directly/indirectly promote plant growth through the production of phytohormones, enzymes and by suppressing phytopathogens and insects. The vast functional and genetic diversity of microbial groups including bacteria, fungi and actinomycetes supports in all the above ways for soil health. This book chapter gives an outline of such microbes and their contribution in promoting soil health and its role as soil health indicators.

Role of Cyanobacteria in Nutrient Cycle and Use Efficiency in the Soil

Cyanobacteria are ancient key photosynthetic prokaryotic organisms playing critical role in the biological nutrient cycling in different habitats. They have tremendous capabilities for the management of agroecosystem. The organism possesses various attributes that directly or indirectly not only improve nitrogen (N), phosphorus (P), potassium (K), iron (Fe), and other mineral content in the soils but facilitate plants to make better use of such minerals in plant growth promotion for enhanced crop production. Although much work has been carried out on the nitrogen fixation mechanisms of cyanobacteria, its direct implication in the field is still awaited. Similarly continuous research work is required on the identification of efficient strains of cyanobacteria to make better utilization of them in improving macro- and micronutrients use efficiency by the plants.

Whole Genome Phylogeny of Prochlorococcus marinus Group of Cyanobacteria: Genome Alignment and Overlapping Gene Approach

Prochlorococcus is the smallest known oxygenic phototrophic marine cyanobacterium dominating the mid-latitude oceans. Physiologically and genetically distinct P. marinus isolates from many oceans in the world were assigned two different groups, a tightly clustered high-light (HL)-adapted and a divergent low-light (LL-) adapted clade. Phylogenetic analysis of this cyanobacterium on the basis of 16S rRNA and other conserved genes did not show consistency with its phenotypic behavior. We analyzed phylogeny of this genus on the basis of complete genome sequences through genome alignment, overlapping-gene content and gene-order approach. Phylogenetic tree of P. marinus obtained by comparing whole genome sequences in contrast to that based on 16S rRNA gene, corresponded well with the HL/LL ecotypic distinction of twelve strains and showed consistency with phenotypic classification of P. marinus. Evidence for the horizontal descent and acquisition of genes within and across the genus was observed. Many genes involved in metabolic functions were found to be conserved across these genomes and many were continuously gained by different strains as per their needs during the course of their evolution. Consistency in the physiological and genetic phylogeny based on whole genome sequence is established. These observations improve our understanding about the adaptation and diversification of these organisms under evolutionary pressure.

Functional profiling of cyanobacterial genomes and its role in ecological adaptations

With the availability of complete genome sequences of many cyanobacterial species, it is becoming feasible to study the broad prospective of the environmental adaptation and the overall changes at transcriptional and translational level in these organisms. In the evolutionary phase, niche-specific competitive forces have resulted in specific features of the cyanobacterial genomes. In this study, functional composition of the 84 different cyanobacterial genomes and their adaptations to different environments was examined by identifying the genomic composition for specific cellular processes, which reflect their genomic functional profile and ecological adaptation. It was identified that among cyanobacterial genomes, metabolic genes have major share over other categories and differentiation of genomic functional profile was observed for the species inhabiting different habitats. The cyanobacteria of freshwater and other habitats accumulate large number of poorly characterized genes. Strain specific functions were also reported in many cyanobacterial members, of which an important feature was the occurrence of phage-related sequences. From this study, it can be speculated that habitat is one of the major factors in giving the shape of functional composition of cyanobacterial genomes towards their ecological adaptations.

Bioinformatics Resources for the Management of Biological Information on Plant Responses Towards Stresses

In natural and agricultural conditions, plants are exposed to multiple stresses that impose severe impact on growth and development. Stress in plants can be considered as a change in growth phage which leads to disturbance of metabolic homeostasis. Plant pathogens result in biotic stresses, whereas environmental stimuli generate multiple abiotic stresses like temperature extremes, drought, chemical toxicity, salinity, heavy metals, oxidative stress and radiation. Plants respond to these stresses and develop better adaptation by activating their intrinsic machinery. Currently, biological research is witnessing increasing development of methods, technologies and implementations for a better mechanistic representation of biological systems. In the era of multi-omics approaches addressing multiple aspects of biological mechanisms shown by plants in response to biotic or abiotic stresses, huge data is emerging out from research work. This data needs proper management, analysis and interpretation in order to decipher plant strategies to combat stresses. In the past decades, a large number of databases, software, tools and web resources were developed to make ease of access for researchers working to decipher plant responses towards stresses. In this chapter we are describing bioinformatics resources which need to describe information on plant responses against stresses. Bioinformatics resources like database of annotated tentative orthologs from crop abiotic stress transcripts, MIPS PlantsDB, GreenPhylDB, Gramene, GCP Comparative Stress Gene Catalog, Plant Stress Gene Database, PASmiR, QlicRice, Rice Stress Gene Catalog, Arabidopsis Stress Responsive Gene Database, STIFDB and STIFDB2 are available to facilitate multi-omics research in this field. Some of these resources are specific to particular plants, whereas others are generalized and contain information about multiple species.

Plant-Microbe Interactions in Agro-Ecological Perspectives

Microbial interactions in soil are considered as one of the most important activities that occur in the terrestrial ecosystem. They affect all the dynamic processes of plants and other living organisms that live near from them either directly or indirectly. There are two types of microbial interaction that occur in soil. The interactions that occur between individuals within the same species are called intraspecific interaction, and those that occur between organisms of different species either two microbial populations or microbial population and plants or animals are called interspecific interactions. Each microorganism could perform more than one type of interaction depending on the sounding environmental conditions, its partner in the interaction. Microbial interactions are very essential for plant growth and health.