Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population.

Jessica M Labonté,Tullis C Onstott,Esta Van Heerden,Thomas L Kieft,Ramunas Stepanauskas,Maggie Lau,Dylan Chivian,K Eric Wommack,Erin K Field

doi:10.3389/fmicb.2015.00349

Abstract

A major fraction of Earth's prokaryotic biomass dwells in the deep subsurface, where cellular abundances per volume of sample are lower, metabolism is slower, and generation times are longer than those in surface terrestrial and marine environments. How these conditions impact biotic interactions and evolutionary processes is largely unknown. Here we employed single cell genomics to analyze cell-to-cell genome content variability and signatures of horizontal gene transfer (HGT) and viral infections in five cells of Candidatus Desulforudis audaxviator, which were collected from a 3 km-deep fracture water in the 2.9 Ga-old Witwatersrand Basin of South Africa. Between 0 and 32% of genes recovered from single cells were not present in the original, metagenomic assembly of Desulforudis, which was obtained from a neighboring subsurface fracture. We found a transposable prophage, a retron, multiple clustered regularly interspaced short palindromic repeats (CRISPRs) and restriction-modification systems, and an unusually high frequency of transposases in the analyzed single cell genomes. This indicates that recombination, HGT and viral infections are prevalent evolutionary events in the studied population of microorganisms inhabiting a highly stable deep subsurface environment.

Highlights

Deep subsurface microorganisms constitute a significant fraction of the living biomass on our planet (Whitman et al, 1998; Kallmeyer et al, 2012), but our knowledge of these microorganisms remains very limited, due to the difficulties in accessing these environments without introducing microbial contamination and to our inabilities to isolate the indigenous microbiota through cultivation (Colwell and D’Hondt, 2013)
This shows that close relatives of Desulforudis inhabit multiple subsurface environments and can coexist with other microbial species, in support of prior, metagenomic evidence (Moser et al, 2003, 2005a; Lin et al, 2006)
D. audaxviator MP104C were similar to genes found in other Firmicutes, such as Desulfotomaculum sp. and Pelotomaculum sp. (Figure 3). Many of these novel regions were in close proximity to transposases (9 cases), tRNA (2 cases), recombinases (2 cases), clustered regularly interspaced short palindromic repeats (CRISPRs) (1 case), and a prophage (1 case), all of which are indicative of recombination and horizontal gene transfer (HGT) (Ochman et al, 2000; Gogarten et al, 2002; Brüssow et al, 2004; Marraffini and Sontheimer, 2010) (Supplementary Figure 2, and Supplementary Table 7). These results indicate a high prevalence of HGT events among autochthonous bacterial populations of the deep subsurface, despite their extremely slow metabolism and generation times that can be hundreds to thousands of years (Phelps et al, 1994; Jørgensen and D’Hondt, 2006; Lin et al, 2006)

Summary

Introduction

Deep subsurface microorganisms constitute a significant fraction of the living biomass on our planet (Whitman et al, 1998; Kallmeyer et al, 2012), but our knowledge of these microorganisms remains very limited, due to the difficulties in accessing these environments without introducing microbial contamination and to our inabilities to isolate the indigenous microbiota through cultivation (Colwell and D’Hondt, 2013). Ribosomal RNA sequences that are near-identical to MP104C have been detected in many subsurface sites outside the Witwatersrand Basin, including in the Fennoscandian Shield in Finland (Itävaara et al, 2011), a deep saline geothermal aquifer in Germany (Lerm et al, 2013), and the Juan de Fuca crustal basalt fluids (Jungbluth et al, 2013). This suggests that D. audaxviator is highly adapted to conditions of the immense deep subsurface environment and has a cosmopolitan distribution. To the best of our knowledge, 16S rRNA sequences have remained the only type of information about Desulforudis from locations outside the Mponeng fracture, leaving its genetic diversity and associated evolutionary and ecological implications largely unknown

Methods

Results

Conclusion