The genome of a subterrestrial nematode reveals an evolutionary strategy for adaptation to heat

Abstract

The nematode Halicephalobus mephisto was originally discovered inhabiting a deep terrestrial aquifer 1.3 km underground. H. mephisto can thrive under conditions of abiotic stress including heat and minimal oxygen, where it feeds on a community of both chemolithotrophic and heterotrophic prokaryotes in an unusual ecosystem isolated from the surface biosphere. Here we report the comprehensive genome and transcriptome of this organism, identifying a signature of adaptation: an expanded repertoire of 70 kilodalton heat-shock proteins (Hsp70) and avrRpt2 induced gene 1 (AIG1) proteins. We find that positive selection has driven the expansion of Hsp70 genes, which are also transcriptionally induced upon growth under heat stress. We further show that AIG1 may have been acquired by horizontal gene transfer (HGT) from a rhizobial fungus. Over one-third of the genes of H. mephisto are novel, highlighting the divergence of this nematode from other sequenced organisms. This work sheds light on the genomic strategies of adaptation to heat in the first complete subterrestrial eukaryotic genome. IntroductionHalicephalobus mephisto was discovered inhabiting a fluid-filled aquifer accessed from the Beatrix Gold Mine in South Africa at 1.3km below the surface 1 . Radiocarbon dating indicates the aquifer water is over 6,000 years old 1 , and the lack of surface 3 H infiltration, a remnant of atmospheric atomic testing, highlights its isolation from the surface biosphere 1 . The water is warm (37°C), alkaline (pH 7.9), hypoxic (0.42 -2.3mg/L dissolved O 2, ), and rich in biogenic methane (CH 4 ) 1-3 . In spite of these challenging conditions, a thriving, complex microbial community exists in this extreme environment including chemolithoautotrophic organisms that extract energy from the subterrestrial rock and fix organic carbon 2,4 . Syntrophic relationships 3 link sulphur-oxidizing denitrifying bacteria, sulfate reducers, methanogens and anaerobic methane oxidizing organisms into a complex mutually reinforcing microbial food web 2 that supports a rich assemblage of eukaryotic opportunistic predators including nematodes, rotifers, and protists 5 . With the exception of H. mephisto none of these eukaryotic organisms have been cultured in the laboratory, and none have had their genomes sequenced and analyzed until now.Nematodes encode small, remarkably dynamic genomes well suited to studies of adaptation 6,7 . Among the most abundant animals on earth, nematodes have adapted to an incredibly diverse set of environments: from hot springs to polar ice, soil, fresh and saltwater 8 , acid seeps 9 , and the deep terrestrial subsurface 1 , with a wealth of comparative genomic data available. Dynamic gene family expansion 6,10 and shrinkage 11 have proven good signatures of evolutionary adaptive selection in crown eukaryotes, including nematoda 12 . Here we have performed comprehensive genomic and transcriptomic studies in H. mephisto, giving a first view of the evolutionary adaptive response to a subterrestrial environment, and have identifi...