Hydrogen Bioenergetics In Yellowstone Geothermal Ecosystem Biology Essay

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This report seeks to summarize and interpret the work done in the paper "Hydrogen and Bioenergetics in the Yellowstone Geothermal Ecosystem" by Spear, J.R. et al. The paper deals with the study done to identify the Geochemical energy budget of the thermophilic microbes in the hot springs of the Yellowstone National Park; by conducting Phylogenetic analysis, Chemical analysis and Thermodynamic analysis. The authors concluded that most of the microbial mass derives its energy for primary productivity from the oxidation of molecular Hydrogen, even in the presence of high concentrations of sulfide.

Hot Springs are springs which have water temperature above 50oC (or 122oF) and are produced due to geo-thermally heated groundwater. These springs which are usually found near volcanically active areas and are of great interest due to the presence of unique thermophilic (heat- loving) microorganisms.

Thermophilic microbes survive in extremely high temperatures (between 45 - 100oC) and contain special enzymes that enable them to function at such high temperatures. These microbes are usually chemo-lithothrophs, meaning that they derive their energy from oxidation of reduced inorganic compounds or organic compounds and not by photosynthesis (which cannot occur at temperatures above 70oC) and thus survive in regions with no light and very less oxygen or anoxic conditions.

Purpose of the Study:

This particular study was conducted in the Yellowstone National Park to answer the basic question of what are the potential energy sources of particular thermophilic communities in the microbial ecosystem in these hot springs. Previous studies [Ball, J. W. et al. (1998)] detected potential energy sources to be sulfide, CH4 and reduced metals such as As [III], Fe [II] and Mn [II], however the authors felt that these findings were inconsistent as none of these chemicals were ubiquitous in the hot springs and in fact, some of the robust microbial communities had little or none of these potential energy sources.

Specific Objectives of the Paper:

To address how the various geochemistry's affect this issue, the authors came up with three specific lines of inference to tackle this issue: (1) Study the phylogenetic composition of the high temperature(>70oC) microbes to assess the relative abundance of the organisms that make up the community. (2) Conduct parallel chemical analyses of the springs and determine the concentration of aqueous molecular hydrogen present. (3) Carry out thermodynamic modeling to evaluate the bioenergetic potentials of available fuels.


To perform the molecular phylogenetic analyses, sediment samples were collected from certain springs and were frozen immediately on liquid nitrogen. In springs with little or no sediment, they collected and froze the biomass that colonized glass slides which had been placed in the hot springs for duration of 48 hrs to 2 months. Community DNA was extracted and Polymerase Chain Reaction (PCR) was done to amplify the DNA. The products were gel purified and cloned and unique sequences were identified using Restriction Fragment Length Polymorphism (RFLP) and were sequenced, aligned and analyzed with the ARB software package. The sequences were deposited in the GenBank database.

The aqueous H2 concentration was measured using a modified bubble stripping method. The bubbles were collected in air tight syringes and transferred to nitrogen charged, H2 impermeable glass septum vials which were sent for analysis of H2, CH4 and CO2 on a RGA3 reduction gas analyzer. To determine actual H2 concentrations, the measured values were adjusted to account for solubility of H2 at high temperatures with Henry's law: CW=CGHC where CW is the concentration of gas in the water, CG is the concentration of gas in the bubble and HC is Henry's constant. However, as Henry's constant decreases by 28% for hydrogen from temperatures 0 to 100oC, values of Henry's constant were determined with Ostwald's expression. Sulfide measurements were conducted with colorimetric assay.

The Thermodynamic modeling was done by quantifying the amount of chemical energy available by using Gibbs Free Energy equation: ΔGr = ΔGro + RT ln Q, where ΔGr is the change in free energy of the reaction, ΔGro is the standard Gibbs free energy and Q is the activity coefficient of compounds involved in the reaction. The values of Q were determined with the measured composition of hot spring fluid assuming activity coefficients to be one due to their dilute nature. Also the distribution of CO2 and sulfide were calculated from the measured concentrations of these compounds.


The main results obtained were: (1) the finding of ubiquitous H2 concentrations which are appropriate for energy metabolism (Basically, finding a Hydrogen driven metabolisim). Other potential energy sources such as Fe [II], Mn [II] and NH4 occur variably, but the energy yield from the microbial oxidation of such compounds is much lesser and thus cannot possibly contribute to the overall budget sustainability and moreover, the deposits of Fe and Mn oxidation are not conspicuous in the hot springs. (2) Phylogenetic analysis revealed that all the communities contained sequences representative of Aquificales which was most abundant and is known to rely on Hydrogen as energy source (3) Hydrogen concentration varied with springs with higher concentrations of Fe[II] and Sulfide. When Sulfate was present, sulfate reducing bacteria contributed significantly to the energy budget of the community. (4) Communities were dominated by both Bacterial rRNA genes and by Archaea on an equal basis (though it is usually presumed that archaea would have been predominant) (5) The thermodynamic modeling which was done comparing the amount of energy available from O2 consuming metabolic reactions showed that H2 oxidation was preferred under oxygen limited conditions. (6) >93% of rRNA sequences characteristic of H2 oxidizing microbes dominate both high and low sulfide springs and δ-Proteobacterial sequences are more abundant in high concentrations.


The paper by Spear et al. is a highly organized paper and is a meticulously set up study which has a number of highlights which make it a very strong scientific-evidence filled paper. The authors also keep referencing previous work to a considerable extent to re-state and give a solid foundation for their results and to also to show novel techniques by using inter-disciplinary research methods.

The paper has the following highlights: (1) Concept of Microbial Ecosystem: This was a concept which was not dealt with prior to this paper. This is a challenging new way of thinking as microbial ecosystems are not constrained by geography or climate but rather by local Chemical and Physical conditions. (2) The Three Step Inference: The paper showed how well a combination-approach worked, which is "compatible with all the data and yet in contrast to what might have been expected." [Nealson (2005)]. (3) Minimization of Potential Experimental Artifacts: The study ensured the minimization of potential experimental artifacts by using different suites of PCR primer with broad specificities, eg: the Obsidian Pool Prime was examined with 8 different primer pairs. (4) The Hydrogen Driven Metabolism: Apart from the excitement of finding the existence of a Hydrogen driven metabolism, this paper references and proves the controversial 1992 paper by Tommy Gold on Deep, Hot Biosphere. The identification of this metabolism has now brought more scientific research into Deep Sub-Surface Biology. (5)Origin of hydrogen in the Yellowstone environment: Nealson states that geochemically produced Hydrogen can occur in two ways: {i} Outgassing of mantle-based rocks, releasing magmatic volatiles in fluids that are neutral or slightly acidic; {ii} Interactions of water with highly reduced ultramafic rocks releasing high pH fluids containing H2 and CH4, but containing much less CO2 because of the high pH. Another theory of the origin of the geothermal hydrogen is {iii} Radioactive decay of naturally occurring elements such as Uranium, Thorium and Potassium split water molecules into Hydrogen and Oxygen. This theory postulated by Mascarelli (2010) also suggests that the same process could have occurred on early Earth.


The Hydrogen Metabolism theory opens doors into Deep sea / Sub-surface Microbiology and Astrobiology. Recent scientists such as Katrina Edwards of University of Southern California are working on microorganisms which are 3 km below the Deep sea surface and a paper published by Lin, L. et al. on Long-Term Sustainability of a High-Energy, Low-Diversity Crustal Biome (2006) focuses on some deep sea surface microbes which are hypothesized to thrive on Hydrogen Metabolism in anoxic conditions and on inorganic substrates. This research helps in understanding topics such as the of origin of life, early Earth conditions and the possibility of life on other planets.


The paper was a well written and documented study, however the only negative point was that raw data was not presented for the reader to completely cross verify the claims.

Through countless studies done in Yellowstone National Park and increasing efforts taken to understand Extremophiles and their metabolisims, whilst still discovering them at places which were considered least habitable brings us to the most difficult question: what exactly are the limits to life?