Biogeochemistry and Ecophysiology of Atmospheric CO and H2

Biotechnological perspective for wireless energy: H2-based power extraction from air

Despite its extreme scarcity, atmospheric H2 serves as an energy source for some prokaryotes. Recently, Grinter, Kropp, et al. reported the structural, biochemical, electrochemical, and spectroscopic elucidation of an underlying H2 catalyst, a [NiFe]-hydrogenase, which, owing to its extremely high affinity, facilitates the extraction of energy from ambient air.

Enriched hydrogen-oxidizing microbiomes show a high diversity of co-existing hydrogen-oxidizing bacteria

While numerous reports exist on the axenic culturing of different hydrogen-oxidizing bacteria (HOB), knowledge about the enrichment of microbial communities growing on hydrogen, oxygen, and carbon dioxide as sole carbon and energy sources remains negligible. We want to elucidate if in such enrichments, most enriched populations are HOBs or heterotrophic organisms. In the present study, bacteria enriched from a soil sample and grown over 5 transfers using a continuous supply of hydrogen, oxygen, and carbon dioxide to obtain an enriched autotrophic hydrogen-oxidizing microbiome. The success of the enrichment was evaluated by monitoring ammonium consumption and biomass concentration for 120 days. The shift in the microbial composition of the original soil inoculum and all transfers was observed based on 16S rRNA amplicon sequencing. The hydrogen-oxidizing facultative chemolithoautotroph Hydrogenophaga electricum was isolated and found to be one of the abundant species in most transfers. Moreover, Achromobacter was isolated both under heterotrophic and autotrophic conditions, which was characterized as a hydrogen-oxidizing bacterium. The HOB enrichment condition constructed in this study provided an environment for HOB to develop and conquer in all transfers. In conclusion, we showed that enrichments on hydrogen, oxygen, and carbon dioxide as sole carbon and energy sources contain a diverse mixture of HOB and heterotrophs that resulted in a collection of culturable isolates. These isolates can be useful for further investigation for industrial applications.

Volcanic Soils as Sources of Novel CO-Oxidizing Paraburkholderia and Burkholderia: Paraburkholderia hiiakae sp. nov., Paraburkholderia metrosideri sp. nov., Paraburkholderia paradisi sp. nov., Paraburkholderia peleae sp. nov., and Burkholderia alpina sp. nov. a Member of the Burkholderia cepacia Complex

Previous studies showed that members of the Burkholderiales were important in the succession of aerobic, molybdenum-dependent CO oxidizing-bacteria on volcanic soils. During these studies, four isolates were obtained from Kilauea Volcano (Hawai‘i, USA); one strain was isolated from Pico de Orizaba (Mexico) during a separate study. Based on 16S rRNA gene sequence similarities, the Pico de Orizaba isolate and the isolates from Kilauea Volcano were provisionally assigned to the genera Burkholderia and Paraburkholderia, respectively. Each of the isolates possessed a form I coxL gene that encoded the catalytic subunit of carbon monoxide dehydrogenase (CODH); none of the most closely related type strains possessed coxL or oxidized CO. Genome sequences for Paraburkholderia type strains facilitated an analysis of 16S rRNA gene sequence similarities and average nucleotide identities (ANI). ANI did not exceed 95% (the recommended cutoff for species differentiation) for any of the pairwise comparisons among 27 reference strains related to the new isolates. However, since the highest 16S rRNA gene sequence similarity among this set of reference strains was 98.93%, DNA-DNA hybridizations (DDH) were performed for two isolates whose 16S rRNA gene sequence similarities with their nearest phylogenetic neighbors were 98.96 and 99.11%. In both cases DDH values were <16%. Based on multiple variables, four of the isolates represent novel species within the Paraburkholderia: Paraburkholderia hiiakae sp. nov. (type strain I2^T = DSM 28029^T = LMG 27952^T); Paraburkholderia paradisi sp. nov. (type strain WA^T = DSM 28027^T = LMG 27949^T); Paraburkholderia peleae sp. nov. (type strain PP52-1^T = DSM 28028^T = LMG 27950^T); and Paraburkholderia metrosideri sp. nov. (type strain DNBP6-1^T = DSM 28030^T = LMG 28140^T). The remaining isolate represents the first CO-oxidizing member of the Burkholderia cepacia complex: Burkholderia alpina sp. nov. (type strain PO-04-17-38^T = DSM 28031^T = LMG 28138^T).

Anaerobic carboxydotrophic bacteria in geothermal springs identified using stable isotope probing

Carbon monoxide (CO) is a potential energy and carbon source for thermophilic bacteria in geothermal environments. Geothermal sites ranging in temperature from 45 to 65°C were investigated for the presence and activity of anaerobic CO-oxidizing bacteria. Anaerobic CO oxidation potentials were measured at up to 48.9 μmoles CO g⁻¹ (wet weight) day⁻¹ within five selected sites. Active anaerobic carboxydotrophic bacteria were identified using ¹³CO DNA stable isotope probing (SIP) combined with pyrosequencing of 16S rRNA genes amplified from labeled DNA. Bacterial communities identified in heavy DNA fractions were predominated by Firmicutes, which comprised up to 95% of all sequences in ¹³CO incubations. The predominant bacteria that assimilated ¹³C derived from CO were closely related (>98% 16S rRNA gene sequence identity) to genera of known carboxydotrophs including Thermincola, Desulfotomaculum, Thermolithobacter, and Carboxydocella, although a few species with lower similarity to known bacteria were also found that may represent previously unconfirmed CO-oxidizers. While the distribution was variable, many of the same OTUs were identified across sample sites from different temperature regimes. These results show that bacteria capable of using CO as a carbon source are common in geothermal springs, and that thermophilic carboxydotrophs are probably already quite well known from cultivation studies.

Microsensor measurements of hydrogen gas dynamics in cyanobacterial microbial mats

We used a novel amperometric microsensor for measuring hydrogen gas production and consumption at high spatio-temporal resolution in cyanobacterial biofilms and mats dominated by non-heterocystous filamentous cyanobacteria (Microcoleus chtonoplastes and Oscillatoria sp.). The new microsensor is based on the use of an organic electrolyte and a stable internal reference system and can be equipped with a chemical sulfide trap in the measuring tip; it exhibits very stable and sulfide-insensitive measuring signals and a high sensitivity (1.5–5 pA per μmol L^-1 H₂). Hydrogen gas measurements were done in combination with microsensor measurements of scalar irradiance, O₂, pH, and H₂S and showed a pronounced H₂ accumulation (of up to 8–10% H₂ saturation) within the upper mm of cyanobacterial mats after onset of darkness and O₂ depletion. The peak concentration of H₂ increased with the irradiance level prior to darkening. After an initial build-up over the first 1–2 h in darkness, H₂ was depleted over several hours due to efflux to the overlaying water, and due to biogeochemical processes in the uppermost oxic layers and the anoxic layers of the mats. Depletion could be prevented by addition of molybdate pointing to sulfate reduction as a major sink for H₂. Immediately after onset of illumination, a short burst of presumably photo-produced H₂ due to direct biophotolysis was observed in the illuminated but anoxic mat layers. As soon as O₂ from photosynthesis started to accumulate, the H₂ was consumed rapidly and production ceased. Our data give detailed insights into the microscale distribution and dynamics of H₂ in cyanobacterial biofilms and mats, and further support that cyanobacterial H₂ production can play a significant role in fueling anaerobic processes like e.g., sulfate reduction or anoxygenic photosynthesis in microbial mats.

HT to HTO conversion and field experiments near Darlington Nuclear Power Generating Station (DNPGS) site

The Canadian input parameters related to tritiated hydrogen gas (HT) used in tritium dose models are currently based on experiments performed at the Chalk River Laboratories (CRL) site in 1986, 1987 and 1994. There is uncertainty in how well other sites experiencing atmospheric HT releases are represented by these data. In order to address this uncertainty, HT to HTO conversion factors were evaluated at different locations near the Darlington Nuclear Power Generating Station (DNPGS) site using various experimental approaches. These were D2 gas exposure chamber experiments, atmospheric tritium measurements, and HTO and OBT measurements in vegetation and soil. In addition to these field experiments, chamber experiments were conducted using HT gas on field soil samples. The suggested Canadian input parameters for atmospheric tritium releases estimate the total fraction of HT oxidized in air and in soil, at the site, to be up to a maximum of 2.4%. Based on the more limited data obtained near DNPGS in early spring, this fraction would likely be closer to 0.5%. The result suggests that current parameters provide a conservative estimate for the DNPGS site.

NITROGEN FIXATION, HYDROGEN CYCLING, AND ELECTRON TRANSPORT KINETICS IN TRICHODESMIUM ERYTHRAEUM (CYANOBACTERIA) STRAIN IMS101(1)

This study describes the relationships between dinitrogen (N2 ) fixation, dihydrogen (H2 ) production, and electron transport associated with photosynthesis and respiration in the marine cyanobacterium Trichodesmium erythraeum Ehrenb. strain IMS101. The ratio of H2 produced:N2 fixed (H2 :N2 ) was controlled by the light intensity and by the light spectral composition and was affected by the growth irradiance level. For Trichodesmium cells grown at 50 μmol photons · m(-2)  · s(-1) , the rate of N2 fixation, as measured by acetylene reduction, saturated at light intensities of 200 μmol photons · m(-2)  · s(-1) . In contrast, net H2 production continued to increase with light levels up to 1,000 μmol photons · m(-2)  · s(-1) . The H2 :N2 ratios increased monotonically with irradiance, and the variable fluorescence measured using a fast repetition rate fluorometer (FRRF) revealed that this increase was accompanied by a progressive reduction of the plastoquinone (PQ) pool. Additions of 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB), an inhibitor of electron transport from PQ pool to PSI, diminished both N2 fixation and net H2 production, while the H2 :N2 ratio increased with increasing level of PQ pool reduction. In the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), nitrogenase activity declined but could be prolonged by increasing the light intensity and by removing the oxygen supply. These results on the coupling of N2 fixation and H2 cycling in Trichodesmium indicate how light intensity and light spectral quality of the open ocean can influence the H2 :N2 ratio and modulate net H2 production.

Cultivation-independent detection of autotrophic hydrogen-oxidizing bacteria by DNA stable-isotope probing

Knallgas bacteria are a physiologically defined group that is primarily studied using cultivation-dependent techniques. Given that current cultivation techniques fail to grow most bacteria, cultivation-independent techniques that selectively detect and identify knallgas bacteria will improve our ability to study their diversity and distribution. We used stable-isotope probing (SIP) to identify knallgas bacteria in rhizosphere soil of legumes and in a microbial mat from Obsidian Pool in Yellowstone National Park. When samples were incubated in the dark, incorporation of (13)CO(2) was H(2) dependent. SIP enabled the detection of knallgas bacteria that were not detected by cultivation, and the majority of bacteria identified in the rhizosphere soils were betaproteobacteria predominantly related to genera previously known to oxidize hydrogen. Bacteria in soil grew on hydrogen at concentrations as low as 100 ppm. A hydB homolog encoding a putative high-affinity NiFe hydrogenase was amplified from (13)C-labeled DNA from both vetch and clover rhizosphere soil. The results indicate that knallgas bacteria can be detected by SIP and populations that respond to different H(2) concentrations can be distinguished. The methods described here should be applicable to a variety of ecosystems and will enable the discovery of additional knallgas bacteria that are resistant to cultivation.

Hydrogen cycling by the unicellular marine diazotroph Crocosphaera watsonii strain WH8501

The hydrogen (H₂) cycle associated with the dinitrogen (N₂) fixation process was studied in laboratory cultures of the marine cyanobacterium Crocosphaera watsonii. The rates of H₂ production and acetylene (C₂H₂) reduction were continuously measured over the diel cycle with simultaneous measurements of fast repetition rate fluorometry and dissolved oxygen. The maximum rate of H₂ production was coincident with the maximum rates of C₂H₂ reduction. Theoretical stoichiometry for N₂ fixation predicts an equimolar ratio of H₂ produced to N₂ fixed. However, the maximum rate of net H₂ production observed was 0.09 nmol H₂ μg chlorophyll a (chl a)⁻¹ h⁻¹) compared to the N₂ fixation rate of 5.5 nmol N₂ μg chl a⁻¹ h⁻¹, with an H₂ production/N₂ fixation ratio of 0.02. The 50-fold discrepancy between expected and observed rates of H₂ production was hypothesized to be a result of H₂ reassimilation by uptake hydrogenase. This was confirmed by the addition of carbon monoxide (CO), a potent inhibitor of hydrogenase, which increased net H₂ production rates ∼40-fold to a maximum rate of 3.5 nmol H₂ μg chl a⁻¹ h⁻¹. We conclude that the reassimilation of H₂ by C. watsonii is highly efficient (> 98%) and hypothesize that the tight coupling between H₂ production and consumption is a consequence of fixing N₂ at nighttime using a finite pool of respiratory carbon and electrons acquired from daytime solar energy capture. The H₂ cycle provides unique insight into N₂ fixation and associated metabolic processes in C. watsonii.

Oxygen-tolerant H2 oxidation by membrane-bound [NiFe] hydrogenases of ralstonia species. Coping with low level H2 in air

Knallgas bacteria such as certain Ralstonia spp. are able to obtain metabolic energy by oxidizing trace levels of H2 using O2 as the terminal electron acceptor. The [NiFe] hydrogenases produced by these organisms are unusual in their ability to oxidize H2 in the presence of O2, which is a potent inactivator of most hydrogenases through attack at the active site. To probe the origin of this unusual O2 tolerance, we conducted a study on the membrane-bound hydrogenase from Ralstonia eutropha H16 and that of the closely related organism Ralstonia metallidurans CH34, which was purified using a new heterologous overproduction system. Direct electrochemical methods were used to determine apparent inhibition constants for O2 inhibition of H2 oxidation (K I(app)O2) for each enzyme. These values were at least 2 orders of magnitude higher than those of "standard" [NiFe] hydrogenases. Amino acids close to the active site were exchanged in the membrane-bound hydrogenase of R. eutropha H16 for those from standard hydrogenases to probe the role of individual residues in conferring O2 sensitivity. Michaelis constants for H2 (K M H2) were determined, and for some mutants these were increased more than 20-fold relative to the wild type. Mutations resulting in membrane-bound hydrogenase enzymes with increased K M H2 or decreased K I(app)O2 values were associated with impaired lithoautotrophic growth in the presence of high O2 concentrations.

Carbon monoxide from composting due to thermal oxidation of biomass

Emissions of carbon monoxide (CO) were observed from decomposing organic wastes and litter under laboratory, pilot composting plant, and natural conditions. Field studies included air from inside a compost heap of about 200 m3, emissions from composting of livestock wastes at a biologically operating farm, and leaf litter pile air samples. The concentration of CO was up to 120 micromol mol(-1) in the compost piles of green waste, and up to 10 micromol mol(-1) in flux chambers above livestock waste windrow composts. The mean CO flux rates were approximately 20 mg CO m(-2) h(-1) for compost heaps of green waste, and varied from 30 to 100 mg CO m(-2) h(-1) for fresh dung windrows. Laboratory studies using a temperature and ventilation-controlled substrate container were performed to elucidate the origin of CO, and included hay samples of fixed moisture content at temperatures between 5 and 65 degrees C, including nonsterilized as well as sterilized samples. The concentration of CO was up to 160 micromol mol(-1) in these experiments, and Arrhenius-type plot analyses resulted in activation energies of 65 kJ mol(-1) for thermochemically produced CO from the nonsterilized compost substrate. Sterilized samples showed dramatically reduced CO2 but virtually unchanged CO emissions, albeit at a slightly lower activation energy, likely a result of the high-temperature sterilization. Though globally and regionally these CO emissions are only a minor source, thermochemically produced CO emissions might affect local air quality in and near composting facilities.

Carbon monoxide uptake kinetics in unamended and long-term nitrogen-amended temperate forest soils

The effect of nitrogen (N) additions on the dynamics of carbon monoxide consumption in temperate forest soils is poorly understood. We measured soil CO profiles, potential rates of CO consumption and uptake kinetics in temperate hardwood and pine control plots and plots amended with 50 and 150 kg N ha-1 year-1 for more than 15 years. Soil profiles of CO concentrations were above atmospheric levels in the high-N plots of both stands, suggesting that in these forest soils the balance between consumption and production may be shifted so that either production is increased or consumption decreased. Highest rates of CO consumption were measured in the organic horizon and decreased with soil depth. In the N-amended plots, CO consumption increased in all but one soil depth of the hardwood stand, but decreased in all soil depths of the pine stand. CO enzyme affinities increased with soil depth in the control plots. However, enzyme affinities in the most active soil depths (organic and 0-5 cm mineral) decreased in response to low levels of N in both stands. In the high-N plots, affinities dramatically-increased in the hardwood stand, but decreased in the organic horizon and increased slightly in the 0-5 cm mineral soil in the pine stand. These findings indicate that long-term N addition either by fertilization or deposition may alter the size, composition and/or physiology of the community of CO consumers so that their ability to act as a sink for atmospheric CO has changed. This change could have a substantial effect on the lifetime of greenhouse gases such as CH4 and therefore the future of Earth's climate.

Soil-atmosphere CO exchanges and microbial biogeochemistry of CO transformations in a Brazilian agricultural ecosystem

Although anthropogenic land use has major impacts on the exchange of soil and atmosphere gas in general, relatively little is known about its impacts on carbon monoxide. We compared soil-atmosphere CO exchanges as a function of land use, crop type, and tillage treatment on an experimental farm in Parãna, Brazil, that is representative of regionally important agricultural ecosystems. Our results showed that cultivated soils consumed CO at rates between 3 and 6 mg of CO m(-2) day(-1), with no statistically significant effect of tillage method or crop. However, CO exchange for a pasture soil was near zero, and an unmanaged woodlot emitted CO at a rate of 9 mg of CO m(-2) day(-1). Neither nitrite, aluminum sulfate, nor methyl fluoride additions affected CO consumption by tilled or untilled soils from soybean plots, indicating that CO oxidation did not depend on ammonia oxidizers and that CO oxidation patterns differed in part from patterns reported for forest soils. The apparent K(m) for CO uptake, 5 to 11 ppm, was similar to values reported for temperate forest soils; V(max) values, approximately 1 micro g of CO g (dry weight)(-1) h(-1), were comparable for woodlot and cultivated soils in spite of the fact that the latter consumed CO under ambient conditions. Short-term (24-h) exposure to elevated levels of CO (10% CO) partially inhibited uptake at lower concentrations (i.e., 100 ppm), suggesting that the sensitivity to CO of microbial populations that are active in situ differs from that of known carboxydotrophs. Soil-free soybean and corn roots consumed CO when they were incubated with 100-ppm concentrations and produced CO when they were incubated with ambient concentrations. These results document for the first time a role for cultivated plant roots in the dynamics of CO in an agricultural ecosystem.

CooA: a heme-containing regulatory protein that serves as a specific sensor of both carbon monoxide and redox state

CooA, the heme-containing carbon monoxide (CO) sensor from the bacterium Rhodospirillum rubrum, is a transcriptional factor that activates expression of certain genes in response to CO. As with other heme proteins, CooA is unable to bind CO when the Fe heme is oxidized, consistent with the fact that some of the regulated gene products are oxygen-labile. Upon reduction, there is an unusual switch of protein ligands to the six-coordinate heme and the reduced heme is able to bind CO. CO binding stabilizes a conformation of the dimeric protein that allows sequence-specific DNA binding, and transcription is activated through contacts between CooA and RNA polymerase. CooA is therefore a novel redox sensor as well as a specific CO sensor. CooA is a homolog of catabolite responsive protein (CRP), whose transcriptionally active conformation has been known for some time. The recent solution of the crystal structure of the CO-free (transcriptionally inactive) form of CooA has allowed insights into the mechanism by which both proteins respond to their specific small-molecule effectors.

Enrichment of high-affinity CO oxidizers in Maine forest soil

Carboxydotrophic activity in forest soils was enriched by incubation in a flowthrough system with elevated concentrations of headspace CO (40 to 400 ppm). CO uptake increased substantially over time, while the apparent K(m) ((app)K(m)) for uptake remained similar to that of unenriched soils (<10 to 20 ppm). Carboxydotrophic activity was transferred to and further enriched in sterile sand and forest soil. The (app)K(m)s for secondary and tertiary enrichments remained similar to values for unenriched soils. CO uptake by enriched soil and freshly collected forest soil was inhibited at headspace CO concentrations greater than about 1%. A novel isolate, COX1, obtained from the enrichments was inhibited similarly. However, in contrast to extant carboxydotrophs, COX1 consumed CO with an (app)K(m) of about 15 ppm, a value comparable to that of fresh soils. Phylogenetic analysis based on approximately 1,200 bp of its 16S rRNA gene sequence suggested that the isolate is an alpha-proteobacterium most closely related to the genera Pseudaminobacter, Aminobacter, and Chelatobacter (98.1 to 98.3% sequence identity).

The role of microbial mats in the production of reduced gases on the early Earth

The advent of oxygenic photosynthesis on Earth may have increased global biological productivity by a factor of 100-1,000 (ref. 1), profoundly affecting both geochemical and biological evolution. Much of this new productivity probably occurred in microbial mats, which incorporate a range of photosynthetic and anaerobic microorganisms in extremely close physical proximity. The potential contribution of these systems to global biogeochemical change would have depended on the nature of the interactions among these mat microorganisms. Here we report that in modern, cyanobacteria-dominated mats from hypersaline environments in Guerrero Negro, Mexico, photosynthetic microorganisms generate H2 and CO-gases that provide a basis for direct chemical interactions with neighbouring chemotrophic and heterotrophic microbes. We also observe an unexpected flux of CH4, which is probably related to H2-based alteration of the redox potential within the mats. These fluxes would have been most important during the nearly 2-billion-year period during which photosynthetic mats contributed substantially to biological productivity-and hence, to biogeochemistry-on Earth. In particular, the large fluxes of H2 that we observe could, with subsequent escape to space, represent a potentially important mechanism for oxidation of the primitive oceans and atmosphere.

High purity 14CH4 generation using the thermophilic acetotrophic methanogen Methanothrix sp. strain CALS-1

Methane-oxidizing activity in natural samples is typically measured by amending 14CH4 to the sample and then following the accumulation of 14CO2. Current biological techniques to synthesize 14CH4 yield significant quantities of 14CO that when oxidized to 14CO2 would artificially inflate the measured methane-oxidizing activity of a sample. We present here a new method to biologically produce highly-pure 14CH4 using Methanothrix sp. Strain CALS-1 which produces very little CO. Using this method, 14CH4 was produced at nearly 100% efficiency and at a high specific activity (2.2 GBq.mmol-1) equal to the parent compound, [2-14C] sodium acetate. Furthermore, only trace quantities of H2 and CO were produced with only one molecule of CO produced for every 17,000 molecules of CH4. When compared to the standard CH4 generation method, this technique produced 97% purer CH4.

Carbon monoxide oxidation by bacteria associated with the roots of freshwater macrophytes

The potential rates and control of aerobic root-associated carbon monoxide (CO) consumption were assessed by using excised plant roots from five common freshwater macrophytes. Kinetic analyses indicated that the maximum potential uptake velocities for CO consumption ranged from 0.4 to 2.7 &mgr;mol of CO g (dry weight)-1 h-1 for the five species. The observed rates were comparable to previously reported rates of root-associated methane uptake. The apparent half-saturation constants for CO consumption ranged from 50 to 370 nM CO; these values are considerably lower than the values obtained for methane uptake. The CO consumption rates reached maximum values at temperatures between 27 and 32 degreesC, and there was a transition to CO production at >/=44 degreesC, most likely as a result of thermochemical organic matter decomposition. Incubation of roots with organic substrates (e.g., 5 mM syringic acid, glucose, alanine, and acetate) dramatically reduced the rate of CO consumption, perhaps reflecting a shift in metabolism by facultative CO oxidizers. Based on responses to a suite of antibiotics, most of the CO consumption (about 90%) was due to eubacteria rather than fungi or other eucaryotes. Based on the results of acetylene inhibition experiments, methanotrophs and ammonia oxidizers were not active CO consumers.

Genetic and physiological characterization of the Rhodospirillum rubrum carbon monoxide dehydrogenase system

A 3.7-kb DNA region encoding part of the Rhodospirillum rubrum CO oxidation (coo) system was identified by using oligonucleotide probes. Sequence analysis of the cloned region indicated four complete or partial open reading frames (ORFs) with acceptable codon usage. The complete ORFs, the 573-bp cooF and the 1,920-bp cooS, encode an Fe/S protein and the Ni-containing carbon monoxide dehydrogenase (CODH), respectively. The four 4-cysteine motifs encoded by cooF are typical of a class of proteins associated with other oxidoreductases, including formate dehydrogenase, nitrate reductase, dimethyl sulfoxide reductase, and hydrogenase activities. The R. rubrum CODH is 67% similar to the beta subunit of the Clostridium thermoaceticum CODH and 47% similar to the alpha subunit of the Methanothrix soehngenii CODH; an alignment of these three peptides shows relatively limited overall conservation. Kanamycin cassette insertions into cooF and cooS resulted in R. rubrum strains devoid of CO-dependent H2 production with little (cooF::kan) or no (cooS::kan) methyl viologen-linked CODH activity in vitro, but did not dramatically alter their photoheterotrophic growth on malate in the presence of CO. Upstream of cooF is a 567-bp partial ORF, designated cooH, that we ascribe to the CO-induced hydrogenase, based on sequence similarity with other hydrogenases and the elimination of CO-dependent H2 production upon introduction of a cassette into this region. From mutant characterizations, we posit that cooH and cooFS are not cotranscribed. The second partial ORF starts 67 bp downstream of cooS and would be capable of encoding 35 amino acids with an ATP-binding site motif.