Dhananjaya P. Singh

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.

Response of Brassica napus and B. juncea germplasm from Australia, China and India to Australian populations of Leptosphaeria maculans

Germplasm from Australia, China and India was screened for resistance to blackleg (phoma stem canker), caused by Leptosphaeria maculans, under Australian field conditions. More than half of the world’s races of L. maculans occur in Australia, and sites were chosen to encompass areas of high race diversity. Plots were sown into the previous season’s L. maculans-infested residues. Significant differences in response were observed among genotypes of both Brassica napus and B. juncea when tested in Victoria, South Australia and Western Australia. Significant differences in response were observed among B. juncea, but not B. napus genotypes, when tested in New South Wales. Differences in the relative degree of expression of host resistance were observed between some test sites in relation to Australian cultivars that either contained major gene-based resistance (e.g. Surpass 400) or those that effectively had only polygenic resistance (e.g. AV-Sapphire, Lantern, Monty, Rainbow and Trigold). Australian genotypes, especially of B. napus, are generally more resistant than the Chinese and Indian genotypes. The majority of the B. juncea genotypes from both China (e.g. Xinyou 5) and India (e.g. Rohini) showed a high level of resistance, while some B. napus genotypes (e.g. 04-P34, P617 and P624 from China) showed at least a low level of resistance. Promising Australian B. napus germplasm in particular may provide high levels of polygenic resistance to both India and China should the disease become established in one or both those countries.

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.

Trends in the codon usage patterns of Chromohalobacter salexigens genes.

Chromohalobacter salexigens, a Gammaproteobacterium belonging to the family Halomonadaceae, shows a broad salinity range for growth. In order to reveal the factors influencing architecture of protein coding genes in C. salexigens, pattern of synonymous codon usage bias has been investigated. Overall codon usage analysis of the microorganism revealed that C and G ending codons are predominantly used in all the genes which are indicative of mutational bias. Multivariate statistical analysis showed that the genes are separated along the first major explanatory axis according to their expression levels and their genomic GC content at the synonymous third positions of the codons. Both NC plot and correspondence analysis on Relative Synonymous Codon Usage (RSCU) indicates that the variation in codon usage among the genes may be due to mutational bias at the DNA level and natural selection acting at the level of mRNA translation. Gene length and the hydrophobicity of the encoded protein also influence the codon usage variation of genes to some extent. A comparison of the relative synonymous codon usage between 10% each of highly and lowly expressed genes determines 23 optimal codons, which are statistically over represented in the former group of genes and may provide useful information for salt-stressed gene prediction and gene-transformation. Furthermore, genes for regulatory functions; mobile and extrachromosomal element functions; and cell envelope are observed to be highly expressed. The study could provide insight into the gene expression response of halophilic bacteria and facilitate establishment of effective strategies to develop salt-tolerant crops of agronomic value.

Seed Bio-priming for Biotic and Abiotic Stress Management

In modern agriculture, advance technologies are being deployed for breaking yield barriers and enhancing crop productivity. Devising varied seed enhancement technologies is an important domain assuring uniform field emergence, better crop stand and realisation of higher yield in different crops. Integration of diverse plant extracts, microbial products and biotic agents through bio-priming for managing seed crop targeting against biotic and abiotic stresses has been considered as a unique approach, as it requires lesser amounts of chemicals, enhances efficacy of the seeds, reduces the cost of management and eliminates pollution hazards while causing minimum interference with biological equilibrium. Seed bio-priming is one of the vital seed enhancement tool in management of biotic as well as abiotic stresses and guarantees uniform stand establishment under stress conditions. Therefore, research programmes encompassing identification and genetic manipulations of novel biocontrol agents (fungal and bacterial strains) along with its commercial application needs to be devised.

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.

Rhizobacteria Mediated Induced Systemic Tolerance in Plants: Prospects for Abiotic Stress Management

The role of plant-growth-promoting rhizobacteria (PGPR) in promotion of plant growth as well as in reducing biotic stress has been well documented. The bacterial determinants of “induced systemic resistance” (ISR) as well as its activation pathways in plants have been significantly evaluated during the past decade. However, the role of PGPRs in “induced systemic tolerance” (IST) to abiotic stresses has only been revealed very recently. Some bacterial determinants were identified for triggering IST in the host as well as some of the genes involved during the process. In certain cases, the ISR and the IST-mediating pathways were shown to be common whereas in some others they were quite different. The overall impact of microbe-mediated elicitation responses in plants, whether at the biochemical, the molecular, or the physical level may lead to protection against biotic and abiotic stresses and, in a cumulative manner, constitutes the basis of ecofriendly stress-management strategy. In the current chapter, we provide a brief overview of PGPR-mediated stress-tolerance responses in plants and the molecular and the cellular mechanisms responsible to alleviate stresses.