Microbial Diversity in Ultra-High-Pressure Rocks and Fluids from the Chinese Continental Scientific Drilling Project in China

Abstract

Microbial communities in ultra-high-pressure (UHP) rocks and drilling fluids from the Chinese Continental Scientific Drilling Project were characterized. The rocks had a porosity of 1 to 3.5% and a permeability of ϳ0.5 mDarcy. Abundant fluid and gas inclusions were present in the minerals. The rocks contained significant amounts of Fe 2 O 3 , FeO, P 2 O 5 , and nitrate (3 to 16 ppm). Acridine orange direct counting and phospholipid fatty acid analysis indicated that the total counts in the rocks and the fluids were 5.2 ؋ 10 3 to 2.4 ؋ 10 4 cells/g and 3.5 ؋ 10 8 to 4.2 ؋ 10 9 cells/g, respectively. Enrichment assays resulted in successful growth of thermophilic and alkaliphilic bacteria from the fluids, and some of these bacteria reduced Fe(III) to magnetite. 16S rRNA gene analyses indicated that the rocks were dominated by sequences similar to sequences of Proteobacteria and that most organisms were related to nitrate reducers from a saline, alkaline, cold habitat; however, some phylotypes were either members of a novel lineage or closely related to uncultured clones. The bacterial communities in the fluids were more diverse and included Proteobacteria, Bacteroidetes, gram-positive bacteria, Planctomycetes, and Candidatus taxa. The archaeal diversity was lower, and most sequences were not related to any known cultivated species. Some archaeal sequences were 90 to 95% similar to sequences recovered from ocean sediments or other subsurface environments. Some archaeal sequences from the drilling fluids were >93% similar to sequences of Sulfolobus solfataricus, and the thermophilic nature was consistent with the in situ temperature. We inferred that the microbes in the UHP rocks reside in fluid and gas inclusions, whereas those in the drilling fluids may be derived from subsurface fluids.Advances in our understanding of the origins, diversity, distributions, and functions of microorganisms in deep, often extreme, subsurface environments are rapidly expanding our knowledge of biogeochemical processes on Earth and beyond. The discovery of novel microorganisms in deep accessible subsurface habitats provides opportunities for discovering new pharmaceuticals, studying biosynthetic processes, remediating contaminated environments, and enhancing energy production. The major obstacles to understanding the subsurface biosphere have been our limited abilities to access the deep subsurface environment, to acquire uncontaminated samples, and to place our knowledge of microorganisms (functional genes and proteins) into an environmental context. Past and current opportunities to address biogeochemical processes have largely been limited to the shallow crust and geographically sparse locations (7,19,30,32). More recently, Onstott et al. (27) studied microbial diversity, abundance, and functions in the metamorphic quartzite and Carbon Leader from deep mines in South Africa. Despite the great caution taken, the authors demonstrated that the samples were still contaminated, but they were able to show that indigenous microorganisms w...

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