Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community

Abstract

The terrestrial deep subsurface is a huge repository of microbial biomass, but in relation to its size and physical heterogeneity, few sites have been investigated in detail. Here, we applied a culture-independent metagenomic approach to characterize the microbial community composition in deep (1500 meters below surface) terrestrial fluids. Samples were collected from a former gold mine in Lead, South Dakota, USA, now Sanford Underground Research Facility (SURF). We reconstructed 74 genomes from metagenomes (MAGs), enabling the identification of common metabolic pathways. Sulfate and nitrate/nitrite reduction were the most common putative energy metabolisms. Complete pathways for autotrophic carbon fixation were found in more than half of the MAGs, with the reductive acetyl-CoA pathway by far the most common. Nearly 40% (29 of 74) of the recovered MAGs belong to bacterial phyla without any cultivated members-microbial dark matter. Three of our MAGs constitute two novel phyla previously only identified in 16 S rRNA gene surveys. The uniqueness of this data set-its physical depth in the terrestrial subsurface, the relative abundance and completeness of microbial dark matter genomes and the overall diversity of this physically deep, dark, community-make it an invaluable addition to our knowledge of deep subsurface microbial ecology.

Figure 1

Diversity of organisms from which genomes from metagenomes (MAGs) were reconstructed from the Sanford Underground Research Facility fluids. Maximum-likelihood phylogenomic analysis of all MAGs >50% complete and select genomes, MAGs and single cell amplified genomes from IMG, NCBI and ggKbase. The scale bar corresponds to 1 substitution per amino-acid position. Each numbered and blue-colored branch represents one MAG identified here. The names of major lineages with MAGs found in SURF fluids are indicated with bold-face font. MAGs belonging to novel phyla for which no reference genomes identified (SURF-CP-1 and SURF-CP-2) are indicated. Black (100%), gray (⩾75%) and white (⩾50%) circles indicate nodes with high local support values, from 1000 replicates.

Figure 2

Functional genes, genome size, GC content and small subunit 16S rRNA presence in MAGs. Heat maps indicate total MAG scaffold size, number of contigs, GC content, completeness and contamination. Presence and absence of all SSU rRNA genes >300 bp and presence of genes encoding functional genes are indicated by black boxes: pmoA, particulate methane monooxygenase; nrfAD, nitrite reductase; norBC, nitric oxide reductase; nosZDFY, nitrous oxide reductase; dsrAB, dissimilatory sulfite reductase; napABC, periplasmic nitrate reductase; narABDG, nitrate reductase; nirBDG, nitrite reductase; hydB, sulfur reductase; phsA, thiosulfate reductase; redH, reductive dehalogenase; ICL, isocitrate lyase.

Figure 3

Identification of carbon fixation capabilities in all MAGs >50% complete. Heat map indicates the percent of signature genes present in six well-characterized carbon fixation pathways. A full list of genes queried is described in Supplementary Table 2.