Obligate lithotrophs (e.g., ammonia oxidizers) and facultative lithotrophs (e.g., CO and hydrogen oxidizers) collectively comprise a phylogenetically diverse functional group that contributes significantly to carbon and nitrogen cycles in soils and plays important roles in trace gas dynamics (e.g., carbon monoxide and nitrous and nitric oxides) that affect tropospheric chemistry and radiative forcing. In spite of their diverse physiologies, facultative and obligate lithotrophs typically possess the Calvin-Benson-Bassham cycle enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisCO). In an effort designed to understand the structure of lithotrophic communities in soil, genomic DNA extracts from surface (0 to 2 cm) and subsurface (5 to 7 cm) soils have been obtained from two sites in a Georgia agroecosystem (peanut and cotton plots) and an unmanaged pine stand (>50 years old). The extracts have been used in PCR amplifications of the cbbL gene for the rubisCO large subunit protein. cbbL PCR products were cloned, sequenced, and subjected to phylogenetic and statistical analyses. Numerous novel lineages affiliated with the form IC clade (one of four form I rubisCO clades), which is typified by facultative lithotrophs, comprised lithotrophic communities from all soils. One of the form IC clone sequences clustered with a form IC clade of ammonia-oxidizing Nitrosospira. Distinct assemblages were obtained from each of the sites and from surface and subsurface soils. The results suggest that lithotrophic populations respond differentially to plant type and land use, perhaps forming characteristic associations. The paucity of clone sequences attributed to ammonia-oxidizing bacteria indicates that even though ammonia oxidation occurs in the various soils, the relevant populations are small compared to those of facultative lithotrophs.Chemolithotrophic bacteria, which use inorganic compounds as electron donors for growth, have been placed into two groups based on their electron donors (for examples, see reference 34). Obligate lithotrophs include sulfide-, sulfur-, metal-, ammonium-, and nitrite-oxidizing bacteria, many of which have been described in detail. Facultative lithotrophs include aerobic hydrogen-and CO-oxidizing bacteria, of which relatively few have been described (for examples, see references 25 and 26).Although chemolithotrophic bacteria exhibit a wide range of physiological and ecological traits, most use the Calvin-BensonBassham pathway to incorporate CO 2 . Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisCO) plays a crucial role in this pathway (10,11,30,31). rubisCO occurs in three related forms (I, II, and III) that vary in structure, catalytic properties, and substrate specificity (14,19,38,39,43,46). Form I, which occurs in all chemolithotrophs in the bacterial domain, has been subdivided into four clades, IA to ID, based on phylogenetic analyses (28,38,39,43). Form II occurs in some chemolithotrophs and phototrophs, while form III is an archaeal enzyme (14, 43). Analyses of form I rubisC...

In situ dissolved carbon monoxide (CO) in oligotrophic waters follows a diel cycle varying from 0.3 to 0.5 nmol L Ϫ1 before dawn to 2.5 to 3 nmol L Ϫ1 in early afternoon, when photo-production of CO exceeds biological CO oxidation and other sinks. Coastal waters may contain up to 15 nmol L Ϫ1 [CO] in the daytime. Assays to measure the rate of CO bio-oxidation typically involve the addition of labeled CO to sealed samples, resulting in CO concentrations that are above ambient levels during incubation (up to 9 nmol L Ϫ1 CO). We find that biological oxidation of CO obeys first-order kinetics when incubated with up to 4 nmol L Ϫ1 [CO] in coastal water samples and up to between 4 and 10.8 nmol L Ϫ1 in oligotrophic waters. At higher [CO], kinetic behavior transitions to zeroorder or saturation kinetics. CO-oxidation rate coefficients obtained in dark incubations were not representative of the entire diurnal period, as others have assumed. Biological CO-oxidation rate coefficients k co measured in dark incubations of Sargasso Sea surface water in summer were 0.020 Ϯ 0.002 h Ϫ1 (mean Ϯ standard deviation) and an order of magnitude greater than those measured in situ during daylight hours (0.002 Ϯ 0.001 h Ϫ1). Dark and in situ rate coefficients in early spring were 0.006 Ϯ 0.004 h Ϫ1 and 0.003 Ϯ 0.001 h Ϫ1

The species diversity, phylogenetic affiliations, and physiological activity rates of carbon monoxide-oxidizing microorganisms were investigated, using new isolates from surface waters collected from the coast of New England and type strains from established collections. A direct isolation method allowed the simultaneous recovery of organisms with different growth rates and nutritional requirements and the identification of marine microorganisms that oxidize CO at an environmentally relevant concentration (42 nM CO). Isolates that oxidized CO at environmentally relevant rates (>4.5 ؋ 10 ؊11 nmol CO oxidized cell ؊1 h ؊1 ) were taxonomically diverse, with representatives in the alpha and gamma subclasses of the Proteobacteria and the phylum Bacteroidetes, and represent a hitherto unreported metabolic function for several diverse microbial types. Isolates and type strains having the greatest specific rates of CO metabolism (1.1 ؋ 10 ؊10 to 2.3 ؋ 10 ؊10 nmol CO oxidized cell ؊1 h ؊1 ) belonged to the Roseobacter-associated clade (RAC) of the alpha subclass of the Proteobacteria. By using triple-labeled slide preparations, differential counts of active CO-oxidizing RAC cells, total RAC cells, and total bacterial cell counts in environmental samples were obtained. RAC organisms were a major component of total cell numbers (36%). Based on the density of active CO-oxidizing RAC cells in natural samples and RAC-specific metabolic activities determined for pure cultures, active CO-oxidizing RAC cells may contribute up to 15% of the total CO oxidation occurring in coastal waters.Sunlight-initiated photodegradation of colored dissolved organic matter is primarily responsible for producing carbon monoxide in sunlit waters (27). The surface waters of the world's oceans are saturated with CO with respect to the atmosphere and are therefore a source of atmospheric CO (8,32). It is likely that microorganisms within the water column consume most autochthonous CO (7), and several biogeochemical studies have estimated the diel, annual, and global rates of microbial CO oxidation as an oceanic CO sink (7,8,17,18,38,39). CO production is typically greater near coastal waters than at open-ocean sites, due to higher colored dissolved organic matter content (19). The mid-day CO concentration of 12 nM (36, 37) at our coastal sampling location in Vineyard Sound, Mass., for example, is up to fivefold higher than the maximum measured in the Sargasso Sea (18, 39). Microbial CO oxidation rate coefficients for coastal waters (0.01 to 0.11 h Ϫ1 ) can be an order of magnitude greater than those measured in oligotrophic environments (0.01 to 0.02 h Ϫ1 ) (36, 37), suggesting the presence of an active CO-oxidizing microbial community near shore.The question of which microorganisms are important contributors to CO bio-oxidation observed in coastal or oceanic surface waters has not been satisfactorily resolved. The identities of the microbes responsible for CO bio-oxidation in marine environments remain unknown, and there exists only circumstantial e...

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