Prevalence of methanogens in the uncultured Sikkim hot spring solfataric mud archaeal microbiome

Abstract

Solfataric mud sediment samples were analyzed from two hot springs of North Sikkim district of the Sikkim Himalayas, located at the north-eastern region of Indian Himalayan Geothermal Belt. Old Yume Samdung hot spring (OYS) and New Yume Samdung hot spring (NYS) are located 4500m above the mean sea level and are one of the highest located hot springs of Sikkim. OYS hot spring had more abundance of archaea than the NYS hot spring. The solfataric mud sediments of NYS had 0.03% and OYS had 1.06% archaeal reads of the whole microbiome. Both the samples were dominated by Euryarchaeota (NYS~85%; OYS~95%) followed by few representatives from Crenarchaeota (NYS~12%; OYS~3%) and Thaumanarchaeota (NYS~2%; OYS~1%). Based on abundance, Methanocaldococcus, Pyrococcus, Archaeoglobus, Methanobacter, and Thermococcus were the predominant genera in both the hot springs. Functional protein reads for Crenarchaeota were found among the orders of Desulfurococcales, Sulfolobales and Thermoproteales; whereas reads for the order Nanoarchaeales belonging to Nanoarchaeota phylum and orders Cenarchaeales; Nitrosopumilales from phylum Thaumarchaeota were present in the samples. Functional metagenomics revealed the methanogens of the hot springs. There were no functional genes detected for methanogenesis in NYS, whereas in the case of OYS it was abundantly present in various orders of Euryarchaeota - Methanobacteriales, Methanococcales, Methanopyrales, and Methanosarcinales. Three types of methanogenesis were found – aceticlastic, methylotrophic and hydrogenotrophic in the OYS metaarchaeome. Methanopyrus kandleri, Methanosarcina acetivorans, Methanothermobacter marburgensis, Methanothermobacter thermautotrophicus, and Methanocaldococcus jannaschii were the dominant methanogens found in the metaarchaeome, based on their functional proteins for methanogenesis.