Siva Karthik Varanasi, Pa Ragul, Sushmitha, Aarthi, Manisha Sajanani, P Koringa, TN Patel
Anand Agricultural University, Hyderabad, India.
Paddy is the world’s most cultivated food crop in India, Uttar Pradesh is the largest producer of rice crop. Paddy field soil samples epitomizes one of the complex soil microbial ecology comprising of the utmost important microbes in the biogeochemical cycles viz., the Nitrogen Fixers, Phosphate solubilizing bacteria, Plant Growth Promoting bacteria (PGPB), Methanogens, Methanotrophs and Endophytes. Revealing the metabolic processes performed by microorganism is crucial to understand and manipulate a specific ecosystem. In the present investigation, we aim to understand the metabolic profile of the microbiome of different soil typeswhich critically vary in their organic matter and nutrient content. We also try to recognize their influences on functionality of the microbiome. Four different paddy soils samples – Red, Terai, Dhankar and Inceptisol soil were collected from North-eastern Uttar Pradesh. DNA was isolated using Epicenter MetaGNome DNA isolation kit. The sequencing was done using GS-FLX Roche 454 Sequencer. We employed four different databases for analysis which included Pfam, Tigrfam, COGs and SEED that are provided by three different metagenomic tools WebCARMA, CAMERA (RAMMCAP) and MgRAST.Metabolic profiling of more than 85,000 reads generated from four different Metagenomes reveals that functions like Nitrogen metabolism, Potassium metabolism, Inorganic ion transport (Calcium, Cadmium, Copper and Nickel) are found to be high in Inceptisol. Stress tolerance related functions like Osmotic Stress, Acid Stress tolerance and cold shock proteins were also found high in Inceptisol. Heat shock proteins were found relatively high in Dhankar soil. Dhankar soil also showed higher percentage of Phosphorus metabolism function and inorganic ion transport (Cobalt, Chromium, Molybdenum and Magnesium). Siderophores production was found high in Red and Dhankar soil. Red soil was also found toharbor relatively higher percentage of Heme and Iron metabolism related organisms. The functional diversity in all the four soil types showed very minute variationssuggesting that all these soil types were good for paddy growth though some unique microgenome made minuscule difference in their fertility. However, based on the conditions, the microbiome of the soil evolves itself to adapt and utilize the nutrients and enrich the soil fertility which leads to higher yield of paddy.Multi-tool Metabolic Profiling reveals that SEED annotations of MgRAST classify a maximum of 36% analysis, whereas Pfamand TIGRfam (CAMERA) was able to annotate a maximum of only 20 and 23 percent respectively. COG classification of both MgRAST and CAMERA were able annotate a maximum of 34%. Conclusion: WebCARMA provides only an outline of the Functional Profile.MgRAST is found to be efficient metabolic profiling options with SEED annotation and provides better Data visualization and data retrieval systems. Read more…