Ravindra Soni

Exploration of Csp Genes from Temperate and Glacier Soils of the Indian Himalayas and In Silico Analysis of Encoding Proteins

The metagenomic Csp library was constructed from the temperate and glacier soils of central Himalaya, India followed by polymerase chain reaction (PCR) amplification. The library was further screened for low-temperature adaptation, and the positive recombinants were sorted out by determining changes in the melting temperature (Tm). A homology search of cloned sequence showed their identity with the Csp genes of Pseudomonas fluorescens, Psychrobacter cryohalolentis K5, and Shewanella spp MR-4. Amino acid sequence analysis annotated the presence of conserved aromatic and basic amino acids as well as RNA binding motifs from the cold shock domain. Furthermore, a PROSITE scan showed a moderate identity of less than 60% with the known cold shock-inducible proteins (ribosomal proteins, rbfA, DEAD-box helicases), cold acclimation protein, and temperature-induced protein (SRP1/TIP1). This study highlighted the prevalence of Csp genes from cold Himalayan environments that can be explored for tailor-made crop constructions in future.

Microbial Inoculants as Biofertilizer

Increasing application of chemical fertilizers in agriculture make country self dependent in food production but it depreciate environment and cause harmful impacts on living beings. The excess uses of these fertilizers in agriculture are costly and have various adverse effects on soil fertility. Further, soil microorganisms play an important role in the plant growth and development by various means viz. nitrogen fixation, phosphate solubilisation, phytohormone production etc. Therefore, bio-inoculants for agriculture purpose i.e. bio-fertilizers could be a better alternative to chemical fertilizers for agricultural as well as environmental sustainability.

Metagenomics of Plant Rhizosphere Microbiome

The rhizosphere is a specific microbial habitat in the soil ecosystem. This is the area where soil swayed by plant roots through plant exudates deposition. Further, rhizosphere and root microbiota provide useful services to their host plant, such as protection from pathogen and enhanced mineral acquirement from nearby soil for plant growth. Microbial communities, usually, interact with each other and their host, so it is important to detain as much of the microbial diversity as possible. It requires the use of modern analytical tools such as metagenomics, which can reveal the functional potential of a rhizosphere microbiome.

Toward the Unculturable Microbes for Sustainable Agricultural Production

The microbes are elemental to maintain the life on the Earth, yet we have very little understanding about the majority of microbial forms present in various environments like soils. As per the information available from published researches, a big portion of microbial wealth is unculturable which may contain several beneficial traits, including the plant growth-promoting activities for sustainable agricultural production. Exploitation of these unculturable microbes can enhance our understanding of present practices of organic agriculture. The only way to exploit this unculturable wealth is the “metagenomics,” the culture-independent approach where we are analyzing microbial DNA extracted directly from an environmental sample.

Stress-Tolerant Beneficial Microbes for Sustainable Agricultural Production

Agriculture sector is a major contributor of national income in India, while ensuring food security and employment. Plant exposure to both biotic and abiotic stresses causes major losses to agricultural production worldwide. Biotic factors mainly include interaction with other pathogenic or parasitic microorganisms and insect pests, whereas abiotic factors include temperature, drought, water logging, and salinity. Microorganisms play an important role in the growth and development of plants. They confer several benefits to the plants and help them to alleviate the stress.

Root-Associated Bacteria: Rhizoplane and Endosphere

Root-associated microbiota, primarily from the region of rhizoplane and endosphere, have an influential role for promoting plant growth and development. These microbial communities either directly or indirectly affect the root and subsequently the whole plant. However, several studies have been conducted to explore the hidden bacterial world found in rhizoplane and endosphere through several novel techniques for determining their role in enhancing plant growth. In the following sections of this chapter, we are going to discuss the present status of root-associated microbial research.

Soil Metagenomics: A Tool for Sustainable Agriculture

Microorganisms are considered as an unlimited, untapped, and intriguing source for development of novel genes, antibiotics, bioinoculants, biocatalysts, etc. Therefore, the identification and characterization of the microbial wealth becomes inevitable. Besides other features of bacteria that are a challenge to health, including increase in pathogenicity, antibiotic resistance, mounting host spectra, and possibility of usage for bioterrorism, it becomes a compulsion. Furthermore, a sustainable agriculture development program that frequently exploits the plant growth-promoting rhizobacteria (PGPR) also requires a correct identification and characterization of agriculturally important microorganisms. Metagenomics is defined as the study of all available genomes in an environment that contains considerably more genetic information than provided by the cultured subset. It also helps in bridging the gap between genetics and ecology, indicating that the genes of a single microorganism are connected to the genes of other members of the community.