Article

Environmental genomics reveals a single-species ecosystem deep within Earth.

Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Science (Impact Factor: 31.48). 10/2008; 322(5899):275-8. DOI: 10.1126/science.1155495
Source: PubMed

ABSTRACT DNA from low-biodiversity fracture water collected at 2.8-kilometer depth in a South African gold mine was sequenced and assembled into a single, complete genome. This bacterium, Candidatus Desulforudis audaxviator, composes >99.9% of the microorganisms inhabiting the fluid phase of this particular fracture. Its genome indicates a motile, sporulating, sulfate-reducing, chemoautotrophic thermophile that can fix its own nitrogen and carbon by using machinery shared with archaea. Candidatus Desulforudis audaxviator is capable of an independent life-style well suited to long-term isolation from the photosphere deep within Earth's crust and offers an example of a natural ecosystem that appears to have its biological component entirely encoded within a single genome.

1 Follower
 · 
198 Views
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The basaltic ocean crust is the largest aquifer system on Earth, yet the rates of biological activity in this environment are unknown. Low-temperature (<100°C) fluid samples were investigated from two borehole observatories in the Juan de Fuca Ridge (JFR) flank, representing a range of upper oceanic basement thermal and geochemical properties. Microbial sulfate reduction rates (SRR) were measured in laboratory incubations with 35S-sulfate over a range of temperatures and the identity of the corresponding sulfate-reducing microorganisms (SRM) was studied by analyzing the sequence diversity of the functional marker dissimilatory (bi)sulfite reductase (dsrAB) gene. We found that microbial sulfate reduction was limited by the decreasing availability of organic electron donors in higher temperature, more altered fluids. Thermodynamic calculations indicate energetic constraints for metabolism, which together with relatively higher cell-specific SRR reveal increased maintenance requirements, consistent with novel species-level dsrAB phylotypes of thermophilic SRM. Our estimates suggest that microbially-mediated sulfate reduction may account for the removal of organic matter in fluids within the upper oceanic crust and underscore the potential quantitative impact of microbial processes in deep subsurface marine crustal fluids on marine and global biogeochemical carbon cycling.
    Frontiers in Microbiology 01/2015; 5(748). DOI:10.3389/fmicb.2014.00748 · 3.94 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Abstract Sulphide concentrations in groundwater play a key role in the long-term reliability of the metal canisters containing the radioactive waste within a disposal facility for nuclear waste. This is because sulphide in the groundwaters circulating in the vicinity of the deposition tunnels can react with copper in the canisters causing corrosion and therefore reducing their expected lifetime; in a worst case scenario erosion of the bentonite buffer material will expose the canister more rapidly to the fracture groundwater. Sulphide in the groundwater is predominantly microbially produced and thereby controlled by the content of oxidised sulphur sources, organics (carbon sources), reductants (mainly Fe(II), DOC, H2 and CH4), and also flow and mixing of different groundwater types. In addition, achieved saturation in respect to amorphous Fe-monosulphide will control the possible maximum values and will also limit the Fe2+ and S2− values in the groundwater. The aim of this report is to assess realistic, representative and reliable sulphide groundwater concentrations at present conditions in Forsmark and also to evaluate possible changes during different climatic conditions covering the repository operation period (some tens to hundreds of years), post closure conditions (some thousand of years) and the proceeding temperate period (some tens of thousands of years) which may be extended due to enhanced greenhouse effects etc. It is expected that this period will be followed by the onset of the next glaciation during which periglacial (permafrost), glacial and postglacial conditions may succeed each other. To achieve these aims, an evaluation is performed of all the sulphide-related data reported from the Forsmark site investigations /Laaksoharju et al. 2008/ and later monitoring campaigns, all of which are stored in the Sicada database. This evaluation shows that values from the Complete Chemical Characterisation (CCC) sampling are usually lower than those measured during the monitoring phase. When both CCC and monitoring values are available from one borehole section two values are used, one representing each of the sampling methods. When time series are measured in the monitoring sections, in most cases the sulphide values are higher in the downhole tubing and in the borehole section compared with groundwater from the surrounding fractures. The routinely carried out removal of five borehole section water volumes prior to monitoring are in most cases inadequate to obtain representative samples from the bedrock fractures, i.e. without elevated sulphide due to contamination from the initial stagnant water from the borehole section. It is, however, assumed that the two groundwater samples from the same water conducting structures, i.e. the sample from the monitoring and the sample from the CCC sampling, the latter usually showing lower sulphide, spans the interval of representative sulphide values in the formation water. For most of the CCC and monitoring sections the last sample in the time series is suggested as representing the ‘best possible’ value. It is worth noting that the plug flow calculations have proven to be very useful in order to judge the water volumes needed to be pumped at each monitored section before obtaining a sample sufficiently representative of the fracture groundwater. Practically all sulphide concentrations at Forsmark are ≤ 0.013 mmol/L (~0.4 mg/L). There is, however, a probability that for some deposition location in the repository the surrounding groundwaters may have sulphide concentrations as high as 0.12 mmol/L (~4 mg/L). In order to estimate canister corrosion rates in the SR-Site during a full glacial cycle, it is recommended that the observed distribution of sulphide in groundwaters at Forsmark during the present temperate conditions should be used. Furthermore, it should be noted that the present sulphide concentrations have been sampled after a recent period of possible intrusion of marine sulphate-rich waters.
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Formation of heat-resistant endospores is a specific property of the members of the phylum Firmicutes (low-G+C Gram-positive bacteria). It is found in representatives of four different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, and Negativicutes, which all encode similar sets of core sporulation proteins. Each of these classes also includes non-spore-forming organisms that sometimes belong to the same genus or even species as their spore-forming relatives. This chapter reviews the diversity of the members of phylum Firmicutes, its current taxonomy, and the status of genome-sequencing projects for various subgroups within the phylum. It also discusses the evolution of the Firmicutes from their apparently spore-forming common ancestor and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, ruminococci) in the course of their adaptation to the saprophytic lifestyle in a nutrient-rich environment. It argues that the systematics of Firmicutes is a rapidly developing area of research that benefits from the evolutionary approaches to the ever-increasing amount of genomic and phenotypic data and allows arranging these data into a common framework.
    12/2013; 1(2):TBS-0015-2012. DOI:10.1128/microbiolspectrum.TBS-0015-2012

Full-text (2 Sources)

Download
85 Downloads
Available from
May 16, 2014