Production and consumption of hydrogen in a eutrophic lake

Hydrogen is a major lifeline for aerobic bacteria

Molecular hydrogen (H₂) is available in trace amounts in most ecosystems through atmospheric, biological, geochemical, and anthropogenic sources. Aerobic bacteria use this energy-dense gas, including at atmospheric concentrations, to support respiration and carbon fixation. While it was thought that aerobic H₂ consumers are rare community members, here we summarize evidence suggesting that they are dominant throughout soils and other aerated ecosystems. Bacterial cultures from at least eight major phyla can consume atmospheric H₂. At the ecosystem scale, H₂ consumers are abundant, diverse, and active across diverse soils and are key primary producers in extreme environments such as hyper-arid deserts. On this basis, we propose that H₂ is a universally available energy source for the survival of aerobic bacteria.

Function of Biohydrogen Metabolism and Related Microbial Communities in Environmental Bioremediation

Hydrogen (H₂) metabolism has attracted considerable interest because the activities of H₂-producing and consuming microbes shape the global H₂ cycle and may have vital relationships with the global cycling of other elements. There are many pathways of microbial H₂ emission and consumption which may affect the structure and function of microbial communities. A wide range of microbial groups employ H₂ as an electron donor to catalyze the reduction of pollutants such as organohalides, azo compounds, and trace metals. Syntrophy coupled mutualistic interaction between H₂-producing and H₂-consuming microorganisms can transfer H₂ and be accompanied by the removal of toxic compounds. Moreover, hydrogenases have been gradually recognized to have a key role in the progress of pollutant degradation. This paper reviews recent advances in elucidating role of H₂ metabolism involved in syntrophy and hydrogenases in environmental bioremediation. Further investigations should focus on the application of bioenergy in bioremediation to make microbiological H₂ metabolism a promising remediation strategy.

Geosphere-biosphere interactions in bio-activity volcanic lakes: evidences from Hule and Rìo Cuarto (Costa Rica)

Hule and Río Cuarto are maar lakes located 11 and 18 km N of Poás volcano along a 27 km long fracture zone, in the Central Volcanic Range of Costa Rica. Both lakes are characterized by a stable thermic and chemical stratification and recently they were affected by fish killing events likely related to the uprising of deep anoxic waters to the surface caused by rollover phenomena. The vertical profiles of temperature, pH, redox potential, chemical and isotopic compositions of water and dissolved gases, as well as prokaryotic diversity estimated by DNA fingerprinting and massive 16S rRNA pyrosequencing along the water column of the two lakes, have highlighted that different bio-geochemical processes occur in these meromictic lakes. Although the two lakes host different bacterial and archaeal phylogenetic groups, water and gas chemistry in both lakes is controlled by the same prokaryotic functions, especially regarding the CO2-CH4 cycle. Addition of hydrothermal CO2 through the bottom of the lakes plays a fundamental priming role in developing a stable water stratification and fuelling anoxic bacterial and archaeal populations. Methanogens and methane oxidizers as well as autotrophic and heterotrophic aerobic bacteria responsible of organic carbon recycling resulted to be stratified with depth and strictly related to the chemical-physical conditions and availability of free oxygen, affecting both the CO2 and CH4 chemical concentrations and their isotopic compositions along the water column. Hule and Río Cuarto lakes were demonstrated to contain a CO2 (CH4, N2)-rich gas reservoir mainly controlled by the interactions occurring between geosphere and biosphere. Thus, we introduced the term of bio-activity volcanic lakes to distinguish these lakes, which have analogues worldwide (e.g. Kivu: D.R.C.-Rwanda; Albano, Monticchio and Averno: Italy; Pavin: France) from volcanic lakes only characterized by geogenic CO2 reservoir such as Nyos and Monoun (Cameroon).

Consumption of atmospheric hydrogen during the life cycle of soil-dwelling actinobacteria

Microbe-mediated soil uptake is the largest and most uncertain variable in the budget of atmospheric hydrogen (H2 ). The diversity and ecophysiological role of soil microorganisms that can consume low atmospheric abundances of H2 with high-affinity [NiFe]-hydrogenases is unknown. We expanded the library of atmospheric H2 -consuming strains to include four soil Harvard Forest Isolate (HFI) Streptomyces spp., Streptomyces cattleya and Rhodococcus equi by assaying for high-affinity hydrogenase (hhyL) genes and quantifying H2 uptake rates. We find that aerial structures (hyphae and spores) are important for Streptomyces H2 consumption; uptake was not observed in S. griseoflavus Tu4000 (deficient in aerial structures) and was reduced by physical disruption of Streptomyces sp. HFI8 aerial structures. H2 consumption depended on the life cycle stage in developmentally distinct actinobacteria: Streptomyces sp. HFI8 (sporulating) and R. equi (non-sporulating, non-filamentous). Strain HFI8 took up H2 only after forming aerial hyphae and sporulating, while R. equi only consumed H2 in the late exponential and stationary phase. These observations suggest that conditions favouring H2 uptake by actinobacteria are associated with energy and nutrient limitation. Thus, H2 may be an important energy source for soil microorganisms inhabiting systems in which nutrients are frequently limited.

hypD as a marker for [NiFe]-hydrogenases in microbial communities of surface waters

Hydrogen is an important trace gas in the atmosphere. Soil microorganisms are known to be an important part of the biogeochemical H2 cycle, contributing 80 to 90% of the annual hydrogen uptake. Different aquatic ecosystems act as either sources or sinks of hydrogen, but the contribution of their microbial communities is unknown. [NiFe]-hydrogenases are the best candidates for hydrogen turnover in these environments since they are able to cope with oxygen. As they lack sufficiently conserved sequence motifs, reliable markers for these enzymes are missing, and consequently, little is known about their environmental distribution. We analyzed the essential maturation genes of [NiFe]-hydrogenases, including their frequency of horizontal gene transfer, and found hypD to be an applicable marker for the detection of the different known hydrogenase groups. Investigation of two freshwater lakes showed that [NiFe]-hydrogenases occur in many prokaryotic orders. We found that the respective hypD genes cooccur with oxygen-tolerant [NiFe]-hydrogenases (groups 1 and 5) mainly of Actinobacteria, Acidobacteria, and Burkholderiales; cyanobacterial uptake hydrogenases (group 2a) of cyanobacteria; H2-sensing hydrogenases (group 2b) of Burkholderiales, Rhizobiales, and Rhodobacterales; and two groups of multimeric soluble hydrogenases (groups 3b and 3d) of Legionellales and cyanobacteria. These findings support and expand a previous analysis of metagenomic data (M. Barz et al., PLoS One 5:e13846, 2010, http://dx.doi.org/10.1371/journal.pone.0013846) and further identify [NiFe]-hydrogenases that could be involved in hydrogen cycling in aquatic surface waters.

A soil actinobacterium scavenges atmospheric H2 using two membrane-associated, oxygen-dependent [NiFe] hydrogenases

In the Earth's lower atmosphere, H2 is maintained at trace concentrations (0.53 ppmv/0.40 nM) and rapidly turned over (lifetime ≤ 2.1 y(-1)). It is thought that soil microbes, likely actinomycetes, serve as the main global sink for tropospheric H2. However, no study has ever unambiguously proven that a hydrogenase can oxidize this trace gas. In this work, we demonstrate, by using genetic dissection and sensitive GC measurements, that the soil actinomycete Mycobacterium smegmatis mc(2)155 constitutively oxidizes subtropospheric concentrations of H2. We show that two membrane-associated, oxygen-dependent [NiFe] hydrogenases mediate this process. Hydrogenase-1 (Hyd1) (MSMEG_2262-2263) is well-adapted to rapidly oxidize H2 at a range of concentrations [Vmax(app) = 12 nmol⋅g⋅dw(-1)⋅min(-1); Km(app) = 180 nM; threshold = 130 pM in the Δhyd23 (Hyd1 only) strain], whereas Hyd2 (MSMEG_2719-2720) catalyzes a slower-acting, higher-affinity process [Vmax(app) = 2.5 nmol⋅g⋅dw(-1)⋅min(-1); Km(app) = 50 nM; threshold = 50 pM in the Δhyd13 (Hyd2 only) strain]. These observations strongly support previous studies that have linked group 5 [NiFe] hydrogenases (e.g., Hyd2) to the oxidation of tropospheric H2 in soil ecosystems. We further reveal that group 2a [NiFe] hydrogenases (e.g., Hyd1) can contribute to this process. Hydrogenase expression and activity increases in carbon-limited cells, suggesting that scavenging of trace H2 helps to sustain dormancy. Distinct physiological roles for Hyd1 and Hyd2 during the adaptation to this condition are proposed. Soil organisms harboring high-affinity hydrogenases may be especially competitive, given that they harness a highly dependable fuel source in otherwise unstable environments.

Dissolved hydrogen and nitrogen fixation in the oligotrophic North Pacific Subtropical Gyre

The production of hydrogen (H2) is an inherent component of biological dinitrogen (N2) fixation, and there have been several studies quantifying H2 production relative to N2 fixation in cultures of diazotrophs. However, conducting the relevant measurements for a field population is more complex as shown by this study of N2 fixation, H2 consumption and dissolved H2 concentrations in the oligotrophic North Pacific Ocean. Measurements of H2 oxidation revealed microbial consumption of H2 was equivalent to 1-7% of ethylene produced during the acetylene reduction assay and 11-63% of (15)N2 assimilation on a molar scale. Varying abundances of Crocosphaera and Trichodesmium as revealed by nifH gene abundances broadly corresponded with diel changes observed in both N2 fixation and H2 oxidation. However, no corresponding changes were observed in the dissolved H2 concentrations which remained consistently supersaturated (147-560%) relative to atmospheric equilibrium. The results from this field study allow the efficiency of H2 cycling by natural populations of diazotrophs to be compared to cultured representatives. The findings indicate that dissolved H2 concentrations may depend not only on the community composition of diazotrophs but also upon relevant environmental parameters such as light intensity or the presence of other H2-metabolizing microorganisms.

Distribution analysis of hydrogenases in surface waters of marine and freshwater environments

Background

Surface waters of aquatic environments have been shown to both evolve and consume hydrogen and the ocean is estimated to be the principal natural source. In some marine habitats, H₂ evolution and uptake are clearly due to biological activity, while contributions of abiotic sources must be considered in others. Until now the only known biological process involved in H₂ metabolism in marine environments is nitrogen fixation.

Principal Findings

We analyzed marine and freshwater environments for the presence and distribution of genes of all known hydrogenases, the enzymes involved in biological hydrogen turnover. The total genomes and the available marine metagenome datasets were searched for hydrogenase sequences. Furthermore, we isolated DNA from samples from the North Atlantic, Mediterranean Sea, North Sea, Baltic Sea, and two fresh water lakes and amplified and sequenced part of the gene encoding the bidirectional NAD(P)-linked hydrogenase. In 21% of all marine heterotrophic bacterial genomes from surface waters, one or several hydrogenase genes were found, with the membrane-bound H₂ uptake hydrogenase being the most widespread. A clear bias of hydrogenases to environments with terrestrial influence was found. This is exemplified by the cyanobacterial bidirectional NAD(P)-linked hydrogenase that was found in freshwater and coastal areas but not in the open ocean.

Significance

This study shows that hydrogenases are surprisingly abundant in marine environments. Due to its ecological distribution the primary function of the bidirectional NAD(P)-linked hydrogenase seems to be fermentative hydrogen evolution. Moreover, our data suggests that marine surface waters could be an interesting source of oxygen-resistant uptake hydrogenases. The respective genes occur in coastal as well as open ocean habitats and we presume that they are used as additional energy scavenging devices in otherwise nutrient limited environments. The membrane-bound H₂-evolving hydrogenases might be useful as marker for bacteria living inside of marine snow particles.

Hydrogen partial pressures in a thermophilic acetate-oxidizing methanogenic coculture

Hydrogen partial pressures were measured in a thermophilic coculture comprised of a eubacterial rod which oxidized acetate to H(2) and CO(2) and a hydrogenotrophic methanogen, Methanobacterium sp. strain THF. Zinder and Koch (S. H. Zinder and M. Koch, Arch. Microbiol. 138:263-272, 1984) originally predicted, on the basis of calculations of Gibbs free energies of reactions, that the H(2) partial pressure near the midpoint of growth of the coculture should be near 4 Pa (ca. 4 x 10 atm; ca. 0.024 muM dissolved H(2)) for both organisms to be able to conserve energy for growth. H(2) partial pressures in the coculture were measured to be between 20 and 50 Pa (0.12 to 0.30 muM) during acetate utilization, approximately one order of magnitude higher than originally predicted. However, when DeltaG(f) (free energy of formation) values were corrected for 60 degrees C by using the relationship DeltaG(f) = DeltaH(f) - TDeltaS (DeltaH(f) is the enthalpy or heat of formation, DeltaS is the entropy value, and T is the temperature in kelvins), the predicted value was near 15 Pa, in closer agreement with the experimentally determined values. The coculture also oxidized ethanol to acetate, a more thermodynamically favorable reaction than oxidation of acetate to CO(2). During ethanol oxidation, the H(2) partial pressure reached values as high as 200 Pa. Acetate was not used until after the ethanol was consumed and the H(2) partial pressure decreased to 40 to 50 Pa. After acetate utilization, H(2) partial pressures fell to approximately 10 Pa and remained there, indicating a threshold for H(2) utilization by the methanogen. Axenic cultures of the acetate-oxidizing organism were combined with pure cultures of either Methanobacterium sp. strain THF or Methanobacterium thermoautotrophicum DeltaH to form reconstituted acetate-oxidizing cocultures. The H(2) partial pressures measured in both of these reconstituted cocultures were similar to those measured in the original acetate-oxidizing rod coculture. Since M. thermoautotrophicum DeltaH did not use formate as a substrate, formate is not necessarily involved in interspecies electron transfer in this coculture.

Hydrogen metabolism by decomposing cyanobacterial aggregates in big soda lake, nevada

Hydrogen production by incubated cyanobacterial epiphytes occurred only in the dark, was stimulated by C(2)H(2), and was inhibited by O(2). Addition of NO(3) inhibited dark, anaerobic H(2) production, whereas the addition of NH(4) inhibited N(2) fixation (C(2)H(2) reduction) but not dark H(2) production. Aerobically incubated cyanobacterial aggregates consumed H(2), but light-incubated rates (3.6 mumol of H(2) g h) were statistically equivalent to dark uptake rates (4.8 mumol of H(2) g h), which were statistically equivalent to dark, anaerobic production rates (2.5 to 10 mumol of H(2) g h). Production rates of H(2) were fourfold higher for aggregates in a more advanced stage of decomposition. Enrichment cultures of H(2)-producing fermentative bacteria were recovered from freshly harvested, H(2)-producing cyanobacterial aggregates. Hydrogen production in these cyanobacterial communities appears to be caused by the resident bacterial flora and not by the cyanobacteria. In situ areal estimates of dark H(2) production by submerged epiphytes (6.8 mumol of H(2) m h) were much lower than rates of light-driven N(2) fixation by the epiphytic cyanobacteria (310 mumol of C(2)H(4) m h).

Gas metabolism evidence in support of the juxtaposition of hydrogen-producing and methanogenic bacteria in sewage sludge and lake sediments

We developed new techniques to measure dissolved H(2) and H(2) consumption kinetics in anoxic ecosystems that were not dependent on headspace measurements or gas transfer-limited experimentation. These H(2) metabolism parameters were then compared with measured methane production rates, and estimates of H(2) production and interspecies H(2) transfer were made. The H(2) pool sizes were 205 and 31 nM in sewage sludge from an anaerobic digestor and in sediments (24 m) from Lake Mendota, respectively. The H(2) turnover rate constants, as determined by using in situ pool sizes and temperatures, were 103 and 31 h for sludge and sediment, respectively. The observed H(2) turnover rate accounted for only 5 to 6% of the expected H(2)-CO(2)-dependent methanogenesis in these ecosystems. Our results are in general agreement with the results reported previously and are used to support the conclusion that most of the H(2)-dependent methanogenesis in these ecosystems occurs as a consequence of direct interspecies H(2) transfer between juxtapositioned microbial associations within flocs or consortia.

Tropospheric H(2) budget and the response of its soil uptake under the changing environment

Molecular hydrogen (H(2)) is an indirect greenhouse gas present at the trace level in the atmosphere. So far, the sum of its sources and sinks is close to equilibrium, but its large-scale utilization as an alternative energy carrier would alter its atmospheric burden. The magnitude of the emissions associated with a future H(2)-based economy is difficult to predict and remains a matter of debate. Previous attempts to predict the impact that a future H(2)-based economy would exert on tropospheric chemistry were realized by considering a steady rate of microbial-mediated soil uptake, which is currently responsible of ~80% of the tropospheric H(2) losses. Although soil uptake, also known as dry deposition is the most important sink for tropospheric H(2), microorganisms involved in the activity remain elusive. Given that microbial-mediated H(2) soil uptake is influenced by several environmental factors, global change should exert a significant effect on the activity and then, assuming a steady H(2) soil uptake rate for the future may be mistaken. Here, we present an overview of tropospheric H(2) sources and sinks with an emphasis on microbial-mediated soil uptake process. Future researches are proposed to investigate the influence that global change would exert on H(2) dry deposition and to identify microorganisms involved H(2) soil uptake activity.

Comparison of diffusion and reaction rates in anaerobic microbial aggregates

The ability of hydrogen diffusion to account for the rates of methane production in microbial aggregates was studied in a defined coculture consisting of a sulfate reducer grown as a syntrophic hydrogen producer in the absence of sulfate and a methanogen. The hydrogen uptake kinetics of the methanogen were determined using the infinite dilution technique. The maximum hydrogen uptake velocity was 7.1 nmol/min/μg protein and the half saturation constant for hydrogen uptake was 386 nmol/liter. A threshold of 28 nmol/liter below which no further hydrogen consumption occurred was observed. The reconstituted co-culture was shown to produce methane at rates similar to mixed culture enrichments grown on lactate. The diffusion model demonstrated that for the particular system studied, the rates of hydrogen diffusion could account for the overall rate of methane production.

Isolation ofBacillus schlegelii, a thermophilic, hydrogen oxidizing, aerobic autotroph, from geothermal and nongeothermal environments

Thermophilic hydrogen-oxidizing strains forming round, terminal endospores were isolated from geothermal areas. They were neutrophilic and facultatively autotrophic. They resembledBacillus schlegelii, a thermophilic hydrogen bacterium found so far only in cold environments. Phenotypic similarities, as well as DNA G+C content and DNA:DNA homologies, clearly revealed that the isolated strains belonged to the taxospeciesB. schlegelii. Hence, the strains ofB. schlegelii found in cold environments are probably allochthonous, their origin being geothermal and volcanic areas.

Influence of pH on microbial hydrogen metabolism in diverse sedimentary ecosystems

Hydrogen transformation kinetic parameters were measured in sediments from anaerobic systems covering a wide range of environmental pH values to assess the influence of pH on hydrogen metabolism. The concentrations of dissolved hydrogen were measured and hydrogen transformation kinetics of the sediments were monitored in the laboratory by monitoring hydrogen consumption progress curves. The hydrogen turnover rate constants (kt) decreased directly as a function of decreasing sediment pH, and the maximum hydrogen uptake velocities (Vmax) varied as a function of pH within each of the trophic states. Conversely, the half-saturation concentrations (Km) were independent of pH. The steady-state hydrogen concentrations were at least 2 orders of magnitude lower than the half-saturation constants for hydrogen uptake. Dissolved hydrogen concentrations were at least fivefold higher in sediments from eutrophic systems than from oligotrophic and dystrophic systems. The rates of hydrogen production determined from the assumption of steady state decreased with sediment pH. These data indicate that progressively lower pH values inhibit microbial hydrogen-producing and -consuming processes within sedimentary ecosystems.