Diverse Mn(II)-Oxidizing Bacteria Isolated from Submarine Basalts at Loihi Seamount

Abstract

Metal-oxidizing bacteria may play a key role in the submarine weathering of volcanic rocks and the formation of ferromanganese crusts. Putative fossil microbes encrusted in Mn oxide phases are commonly observed on volcanic glasses recovered from the deep ocean; however, no known Mn(II)-oxidizing bacteria have been directly identified or cultured from natural weathered basalts. To isolate epilithic Mn(II) oxidizing bacteria, we collected young, oxidized pillow basalts from the cold, outer portions of Loihi Seamount, and from nearby exposures of pillow basalts at South Point and Kealakekua Bay, HI. SEM imaging, EDS spectra and X-ray absorption spectroscopy data show that microbial biofilms and associated Mn oxides were abundant on the basalt surfaces. Using a series of seawater-based media that range from highly oligotrophic to organic-rich, we have obtained 26 mesophilic, heterotrophic Mn(II)-oxidizing isolates dominated by α- and γ-Proteobacteria, such as Sulfitobacter, Methylarcula and Pseudoalteromonas spp. Additional isolates include Microbulbifer, Alteromonas, Marinobacter, and Halomonas spp. None of the isolates, nor their closest relatives, were previously recognized as Mn(II) oxidizing bacteria. The physiological function of Mn(II) oxidation is clearly spread amongst many phylogenetically diverse organisms colonizing basalt surfaces. Our findings support a biological catalysis of Mn(II) oxidation during basalt-weathering, and suggest heterotrophic Mn(II) oxidizing bacteria may be ubiquitously associated with submarine glasses within epilithic and endolithic biofilms.     

cumA multicopper oxidase genes from diverse Mn(II)-oxidizing and non-Mn(II)-oxidizing Pseudomonas strains

A multicopper oxidase gene, cumA, required for Mn(II) oxidation was recently identified in Pseudomonas putida strain GB-1. In the present study, degenerate primers based on the putative copper-binding regions of the cumA gene product were used to PCR amplify cumA gene sequences from a variety of Pseudomonas strains, including both Mn(II)-oxidizing and non-Mn(II)-oxidizing strains. The presence of highly conserved cumA gene sequences in several apparently non-Mn(II)-oxidizing Pseudomonas strains suggests that this gene may not be expressed, may not be sufficient alone to confer the ability to oxidize Mn(II), or may have an alternative function in these organisms. Phylogenetic analysis of both CumA and 16S rRNA sequences revealed similar topologies between the respective trees, including the presence of several distinct phylogenetic clusters. Overall, our results indicate that both the cumA gene and the capacity to oxidize Mn(II) occur in phylogenetically diverse Pseudomonas strains.     

cumA, a Gene Encoding a Multicopper Oxidase, Is Involved in Mn2+ Oxidation in Pseudomonas putida GB-1

Pseudomonas putida GB-1-002 catalyzes the oxidation of Mn²⁺. Nucleotide sequence analysis of the transposon insertion site of a nonoxidizing mutant revealed a gene (designated cumA) encoding a protein homologous to multicopper oxidases. Addition of Cu²⁺ increased the Mn²⁺-oxidizing activity of the P. putida wild type by a factor of approximately 5. The growth rates of the wild type and the mutant were not affected by added Cu²⁺. A second open reading frame (designated cumB) is located downstream from cumA. Both cumA and cumB probably are part of a single operon. The translation product of cumB was homologous (level of identity, 45%) to that of orf74 of Bradyrhizobium japonicum. A mutation in orf74 resulted in an extended lag phase and lower cell densities. Similar growth-related observations were made for the cumA mutant, suggesting that the cumA mutation may have a polar effect on cumB. This was confirmed by site-specific gene replacement in cumB. The cumB mutation did not affect the Mn²⁺-oxidizing ability of the organism but resulted in decreased growth. In summary, our data indicate that the multicopper oxidase CumA is involved in the oxidation of Mn²⁺ and that CumB is required for optimal growth of P. putida GB-1-002.     

Identification of Mn(II)-Oxidizing Bacteria from a Low-pH Contaminated Former Uranium Mine

Biological Mn oxidation is responsible for producing highly reactive and abundant Mn oxide phases in the environment that can mitigate metal contamination. However, little is known about Mn oxidation in low-pH environments, where metal contamination often is a problem as the result of mining activities. We isolated two Mn(II)-oxidizing bacteria (MOB) at pH 5.5 (Duganella isolate AB_14 and Albidiferax isolate TB-2) and nine strains at pH 7 from a former uranium mining site. Isolate TB-2 may contribute to Mn oxidation in the acidic Mn-rich subsoil, as a closely related clone represented 16% of the total community. All isolates oxidized Mn over a small pH range, and isolates from low-pH samples only oxidized Mn below pH 6. Two strains with different pH optima differed in their Fe requirements for Mn oxidation, suggesting that Mn oxidation by the strain found at neutral pH was linked to Fe oxidation. Isolates tolerated Ni, Cu, and Cd and produced Mn oxides with similarities to todorokite and birnessite, with the latter being present in subsurface layers where metal enrichment was associated with Mn oxides. This demonstrates that MOB can be involved in the formation of biogenic Mn oxides in both moderately acidic and neutral pH environments.     

Multicopper oxidase involvement in both Mn(II) and Mn(III) oxidation during bacterial formation of MnO2

Global cycling of environmental manganese requires catalysis by bacteria and fungi for MnO₂ formation, since abiotic Mn(II) oxidation is slow under ambient conditions. Genetic evidence from several bacteria indicates that multicopper oxidases (MCOs) are required for MnO₂ formation. However, MCOs catalyze one-electron oxidations, whereas the conversion of Mn(II) to MnO₂ is a two-electron process. Trapping experiments with pyrophosphate (PP), a Mn(III) chelator, have demonstrated that Mn(III) is an intermediate in Mn(II) oxidation when mediated by exosporium from the Mn-oxidizing bacterium Bacillus SG-1. The reaction of Mn(II) depends on O₂ and is inhibited by azide, consistent with MCO catalysis. We show that the subsequent conversion of Mn(III) to MnO₂ also depends on O₂ and is inhibited by azide. Thus, both oxidation steps appear to be MCO-mediated, likely by the same enzyme, which is indicated by genetic evidence to be the MnxG gene product. We propose a model of how the manganese oxidase active site may be organized to couple successive electron transfers to the formation of polynuclear Mn(IV) complexes as precursors to MnO₂ formation.     

Direct Identification of a Bacterial Manganese(II) Oxidase, the Multicopper Oxidase MnxG, from Spores of Several Different Marine Bacillus Species

Microorganisms catalyze the formation of naturally occurring Mn oxides, but little is known about the biochemical mechanisms of this important biogeochemical process. We used tandem mass spectrometry to directly analyze the Mn(II)-oxidizing enzyme from marine Bacillus spores, identified as an Mn oxide band with an in-gel activity assay. Nine distinct peptides recovered from the Mn oxide band of two Bacillus species were unique to the multicopper oxidase MnxG, and one peptide was from the small hydrophobic protein MnxF. No other proteins were detected in the Mn oxide band, indicating that MnxG (or a MnxF/G complex) directly catalyzes biogenic Mn oxide formation. The Mn(II) oxidase was partially purified and found to be resistant to many proteases and active even at high concentrations of sodium dodecyl sulfate. Comparative analysis of the genes involved in Mn(II) oxidation from three diverse Bacillus species revealed a complement of conserved Cu-binding regions not present in well-characterized multicopper oxidases. Our results provide the first direct identification of a bacterial enzyme that catalyzes Mn(II) oxidation and suggest that MnxG catalyzes two sequential one-electron oxidations from Mn(II) to Mn(III) and from Mn(III) to Mn(IV), a novel type of reaction for a multicopper oxidase.     

Indirect Oxidation of Co(II) in the Presence of the Marine Mn(II)-Oxidizing Bacterium Bacillus sp. Strain SG-1

Cobalt(II) oxidation in aquatic environments has been shown to be linked to Mn(II) oxidation, a process primarily mediated by bacteria. This work examines the oxidation of Co(II) by the spore-forming marine Mn(II)-oxidizing bacterium Bacillus sp. strain SG-1, which enzymatically catalyzes the formation of reactive nanoparticulate Mn(IV) oxides. Preparations of these spores were incubated with radiotracers and various amounts of Co(II) and Mn(II), and the rates of Mn(II) and Co(II) oxidation were measured. Inhibition of Mn(II) oxidation by Co(II) and inhibition of Co(II) oxidation by Mn(II) were both found to be competitive. However, from both radiotracer experiments and X-ray spectroscopic measurements, no Co(II) oxidation occurred in the complete absence of Mn(II), suggesting that the Co(II) oxidation observed in these cultures is indirect and that a previous report of enzymatic Co(II) oxidation may have been due to very low levels of contaminating Mn. Our results indicate that the mechanism by which SG-1 oxidizes Co(II) is through the production of the reactive nanoparticulate Mn oxide.     

Cr(III) Oxidation and Cr Toxicity in Cultures of the Manganese(II)-Oxidizing Pseudomonas putida Strain GB-1

Abstract

Mn oxides have long been considered the primary environmental oxidant of Cr(III), however, since most of the reactive Mn oxides in the environment are believed to be of biological origin, microorganisms may indirectly mediate Cr(III) oxidation and accelerate the rate over that seen in purely abiotic systems. In this study, we examined the ability of the Mn(II)-oxidizing bacterium, Pseudomonas putida strain GB-1, to oxidize Cr(III). Our results show that GB-1 cannot oxidize Cr(III) directly, but that in the presence of Mn(II), Cr(III) can be rapidly and completely oxidized. Growth studies suggest that in growth medium with few organics the resulting Cr(VI) may be less toxic to P. putida GB-1 than Cr(III), which is generally considered less hazardous. In addition, Cr(III) present during the growth of P. putida GB-1 appeared to cause iron stress as determined by the production of the fluorescent siderophore pyoverdine. When stressed by Fe limitation or Cr(III) toxicity, Mn(II) oxidation by GB-1 is inhibited.     

A Novel Extracellular Multicopper Oxidase from Phanerochaete chrysosporium with Ferroxidase Activity

Lignin degradation by the white rot basidiomycete Phanerochaete chrysosporium involves various extracellular oxidative enzymes, including lignin peroxidase, manganese peroxidase, and a peroxide-generating enzyme, glyoxal oxidase. Recent studies have suggested that laccases also may be produced by this fungus, but these conclusions have been controversial. We identified four sequences related to laccases and ferroxidases (Fet3) in a search of the publicly available P. chrysosporium database. One gene, designated mco1, has a typical eukaryotic secretion signal and is transcribed in defined media and in colonized wood. Structural analysis and multiple alignments identified residues common to laccase and Fet3 sequences. A recombinant MCO1 (rMCO1) protein expressed in Aspergillus nidulans had a molecular mass of 78 kDa, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and the copper I-type center was confirmed by the UV-visible spectrum. rMCO1 oxidized various compounds, including 2,2′-azino(bis-3-ethylbenzthiazoline-6-sulfonate) (ABTS) and aromatic amines, although phenolic compounds were poor substrates. The best substrate was Fe²⁺, with a K_m close to 2 μM. Collectively, these results suggest that the P. chrysosporium genome does not encode a typical laccase but rather encodes a unique extracellular multicopper oxidase with strong ferroxidase activity.     

NADPH Oxidase Genes from Tomato (Lycopersicon esculentum) and Curly-Leaf Pondweed (Potamogeton crispus)

Abstract: The oxidative burst is an integral component of plant resistance to pathogens. There is accumulating evidence that the oxidative burst is catalyzed by an enzyme with similarities to the phagocyte NADPH oxidase. We have cloned a full length homolog of the gp91 ( phox ) subunit of the plasma membrane NADPH oxidase complex from tomato named LeRBOM. The predicted protein contains 989 amino acids. The large N-terminal domain contains two EF hand calcium binding motifs and one conserved glycosylation site. Six putative membrane spans are present in the C-terminal half of the predicted protein. Extensive homology with the human gp91 ( phox ) subunit was found including conservation of amino acid residues important for heme coordination and substrate binding. We have also isolated partial genomic clones from tomato and from the aquatic plant Potamogeton crispus. These species serve as models for studies of signal transduction leading to NADPH oxidase activation. In tomato, LeRBOH1 expression was too low to be detected on Northern blots. RT-PCR indicated that LeRBOH1 was expressed in all tissues tested.     

Physiological and Genomic Characterization of a Nitrate-Reducing Fe(II)-Oxidizing Bacterium Isolated from Paddy Soil

In this study, a neutrophilic, heterotrophic bacterium (strain Paddy-2) that is capable of ferrous iron [Fe(II)] oxidation coupled with nitrate (NO₃^?) reduction (NRFO) under anoxic conditions was isolated from paddy soil. The molecular identification by 16S rRNA gene sequencing identified the strain as Cupriavidus metallidurans. Strain Paddy-2 reduced 97.7% of NO₃^?and oxidized 89.7% of Fe(II) over 6?days with initial NaNO₃ and FeCl₂ concentrations of 9.37?mM and 4.72?mM, respectively. Acetate (5?mM) was also supplied as a carbon source and an alternative electron donor. A poorly crystalline Fe(III) mineral was the main component observed after 15?days of growth in culture, whereas lepidocrocite was detected in the X-ray diffraction spectrum after 3?months of culture. The homologous genes in electron transfer during Fe(II) oxidation (cyc1, cymA, FoxY, FoxZ, and mtoD) were also identified in the genomes of strain Paddy-2 and other reported NRFO bacteria. These genes encoding c-Cyts may play a role in electron transfer during the process of NRFO. These results provide evidence for the potential of NO₃^? to affect Fe(II) oxidation and biomineralization in bacterium from anoxic paddy soil.     

Manganese(II)-Oxidizing Bacillus Spores in Guaymas Basin Hydrothermal Sediments and Plumes

Microbial oxidation and precipitation of manganese at deep-sea hydrothermal vents are important oceanic biogeochemical processes, yet nothing is known about the types of microorganisms or mechanisms involved. Here we report isolation of a number of diverse spore-forming Mn(II)-oxidizing Bacillus species from Guaymas Basin, a deep-sea hydrothermal vent environment in the Gulf of California, where rapid microbially mediated Mn(II) oxidation was previously observed. mnxG multicopper oxidase genes involved in Mn(II) oxidation were amplified from all Mn(II)-oxidizing Bacillus spores isolated, suggesting that a copper-mediated mechanism of Mn(II) oxidation could be important at deep-sea hydrothermal vents. Phylogenetic analysis of 16S rRNA and mnxG genes revealed that while many of the deep-sea Mn(II)-oxidizing Bacillus species are very closely related to previously recognized isolates from coastal sediments, other organisms represent novel strains and clusters. The growth and Mn(II) oxidation properties of these Bacillus species suggest that in hydrothermal sediments they are likely present as spores that are active in oxidizing Mn(II) as it emerges from the seafloor.     

植物多铜氧化酶及其亚家族成员SKS蛋白

多铜氧化酶包括抗坏血酸氧化酶、漆酶、血浆铜蓝蛋白等多种类型,是植物体内非常重要的一类金属氧化酶,并在植物多种生理过程中发挥着举足轻重的作用。SKS(The skewed5simliar)蛋白是多铜氧化酶家族中一类缺乏铜离子连接所必需的组氨酸残基的特殊成员,由于缺失正常的多铜氧化酶酶活性中心,可能在植物发育中被赋予了新的功能。本文就多铜氧化酶铜离子连接位点、底物选择、演化过程以及植物SKS家族基因的研究进行了阐述。     

Cobalt(II) Oxidation by the Marine Manganese(II)-Oxidizing Bacillus sp. Strain SG-1

The geochemical cycling of cobalt (Co) has often been considered to be controlled by the scavenging and oxidation of Co(II) on the surface of manganese [Mn(III,IV)] oxides or manganates. Because Mn(II) oxidation in the environment is often catalyzed by bacteria, we have investigated the ability of Mn(II)-oxidizing bacteria to bind and oxidize Co(II) in the absence of Mn(II) to determine whether some Mn(II)-oxidizing bacteria also oxidize Co(II) independently of Mn oxidation. We used the marine Bacillus sp. strain SG-1, which produces mature spores that oxidize Mn(II), apparently due to a protein in their spore coats (R.A. Rosson and K. H. Nealson, J. Bacteriol. 151:1027-1034, 1982; J. P. M. de Vrind et al., Appl. Environ. Microbiol. 52:1096-1100, 1986). A method to measure Co(II) oxidation using radioactive ⁵⁷Co as a tracer and treatments with nonradioactive (cold) Co(II) and ascorbate to discriminate bound Co from oxidized Co was developed. SG-1 spores were found to oxidize Co(II) over a wide range of pH, temperature, and Co(II) concentration. Leucoberbelin blue, a reagent that reacts with Mn(III,IV) oxides forming a blue color, was found to also react with Co(III) oxides and was used to verify the presence of oxidized Co in the absence of added Mn(II). Co(II) oxidation occurred optimally around pH 8 and between 55 and 65°C. SG-1 spores oxidized Co(II) at all Co(II) concentrations tested from the trace levels found in seawater to 100 mM. Co(II) oxidation was found to follow Michaelis-Menten kinetics. An Eadie-Hofstee plot of the data suggests that SG-1 spores have two oxidation systems, a high-affinity-low-rate system (K_m, 3.3 × 10^-8 M; V_max, 1.7 × 10^-15 M · spore^-1 · h^-1) and a low-affinity-high-rate system (K_m, 5.2 × 10^-6 M; V_max, 8.9 × 10^-15 M · spore^-1 · h^-1). SG-1 spores did not oxidize Co(II) in the absence of oxygen, also indicating that oxidation was not due to abiological Co(II) oxidation on the surface of preformed Mn(III,IV) oxides. These results suggest that some microorganisms may directly oxidize Co(II) and such biological activities may exert some control on the behavior of Co in nature. SG-1 spores may also have useful applications in metal removal, recovery, and immobilization processes.     

Composition and Activity of an Autotrophic Fe(II)-Oxidizing,Nitrate-Reducing Enrichment Culture

16S rRNA gene libraries from the lithoautotrophic Fe(II)-oxidizing, nitrate-reducing enrichment culture described by Straub et al. (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl. Environ. Microbiol. 62:1458-1460, 1996) were dominated by a phylotype related (95% 16S rRNA gene homology) to the autotrophic Fe(II) oxidizer Sideroxydans lithotrophicus. The libraries also contained phylotypes related to known heterotrophic nitrate reducers Comamonas badia, Parvibaculum lavamentivorans, and Rhodanobacter thiooxidans. The three heterotrophs were isolated and found to be capable of only partial (12 to 24%) Fe(II) oxidation, suggesting that the Sideroxydans species has primary responsibility for Fe(II) oxidation in the enrichment culture.A variety of microorganisms oxidize Fe(II) with nitrate under anaerobic, circumneutral pH conditions (29) and may contribute to an active microbially driven anoxic Fe redox cycle (1, 27-29, 31, 32). Straub et al. (28) obtained the first Fe(II)-oxidizing, nitrate-reducing (enrichment) culture capable of fully autotrophic growth by a reaction such as 5Fe²⁺ + NO₃⁻ + 12H₂O → 5Fe(OH)₃ + 0.5N₂ + 9H⁺. This process has since been demonstrated in detail with the hyperthermophilic archaeon Ferroglobus placidus (9) and with the mesophilic Proteobacteria Chromobacterium violacens strain 2002 (34) and Paracoccus ferrooxidans strain BDN-1 (16). Nitrate-dependent Fe(II) oxidation in the presence of fixed carbon has been documented for Dechlorosoma suillum strain PS (4), Geobacter metallireducens (7), Desulfitobacterium frappieri (23), and Acidovorax strain BoFeN1 (15). In addition to oxidizing insoluble Fe(II)-bearing minerals (33), the enrichment culture described by Straub et al. (28) is the only autotrophic Fe(II)-oxidizing, nitrate-reducing culture capable of near-complete oxidation of uncomplexed Fe(II) with reduction of nitrate to N₂. During Fe(II) oxidation, F. placidus reduces nitrate to nitrite, which may play a significant role in overall Fe(II) oxidation. Although both C. violacens and Paracoccus ferrooxidans reduce nitrate to N₂, C. violacens oxidizes only 20 to 30% of the initial Fe(II), and P. ferrooxidans uses FeEDTA²⁻ but not free (uncomplexed) Fe(II) in medium analogous to that used for cultivation of the enrichment culture described by Straub et al. (28). The enrichment culture described by Straub et al. (28) is thus the most robust culture capable of autotrophic growth coupled to nitrate-dependent Fe(II) oxidation available at present. The composition and activity of this culture was investigated with molecular and cultivation techniques. The culture examined is one provided by K. L. Straub to E. E. Roden in 1998 for use in studies of nitrate-dependent oxidation of solid-phase Fe(II) compounds (33) and has been maintained in our laboratory since that time.     

DNA gyrase (Topoisomerase II) from Pseudomonas aeruginosa

DNA gyrase (Topoisomerase II) has been purified from Pseudomonas aeruginosa strain PAO. This enzyme is inhibited by novobiocin and nalidixic acid. DNA gyrase from P. aeruginosa is resistant to a much higher level of nalidixic acid than is Escherichia coli DNA gyrase. This increased level of resistance may explain, at least in part, the higher levels of natural resistance exhibited by P. aeruginosa toward nalidixic acid.     

Genome Sequence of Fulvimarina pelagi HTCC2506T,a Mn(II)-Oxidizing Alphaproteobacterium Possessing an Aerobic Anoxygenic Photosynthetic Gene Cluster and Xanthorhodopsin

Fulvimarina pelagi is a Mn(II)-oxidizing marine heterotrophic bacterium in the order Rhizobiales. Here we announce the draft genome sequence of F. pelagi HTCC2506^T, which was isolated from the Sargasso Sea by using dilution-to-extinction culturing. The genome sequence contained a xanthorhodopsin gene as well as a photosynthetic gene cluster, which suggests the coexistence of two different phototrophic mechanisms in a single microorganism.Besides being mediated by the well-known process of aerobic oxygenic photosynthesis, utilization of light energy in the marine carbon and nutrient cycling processes is usually mediated by aerobic anoxygenic phototrophic bacteria (AAPB) or prokaryotes containing microbial rhodopsin family proteins (18). AAPB comprise about 10% of total microbial cells in the euphotic zone of diverse marine regimes, with alpha-, beta-, and gammaproteobacteria as major constituents (8, 10). Rhodopsin family proteins, including bacteriorhodopsin, proteorhodopsin, and xanthorhodopsin (XR), have been shown to exist in 7 to 70% of marine prokaryotes and contribute photoheterotrophy in diverse phylogenetic groups such as Flavobacteria, Proteobacteria, and Archaea (15, 19). However, no single microorganism has been reported to contain the genes for both aerobic anoxygenic phototrophy (AAnP) and rhodopsin family proteins.F. pelagi HTCC2506^T was cultivated through a dilution-to-extinction approach (3) from the western Sargasso Sea and identified as a novel genus and species in the order Rhizobiales of the Alphaproteobacteria by polyphasic taxonomy (2). Later, three F. pelagi strains, including HTCC2506^T, were shown to have Mn(II)-oxidizing activity (1). The draft genome sequence of HTCC2506^T was determined by shotgun sequencing at the J. Craig Venter Institute as part of the Moore Foundation Microbial Genome Sequencing Project and analyzed by the GenDB annotation program (17) at the Center for Genome Research and Biocomputing at Oregon State University and the Joint Genome Institute IMG system (http://img.jgi.doe.gov) (14).The draft genome was 3,802,689 bp in length, distributed in 20 contigs with 61.2% G+C content, and contained 3,754 protein-coding genes, three copies of 16S-23S-5S rRNA genes, and 54 tRNA genes. Remarkably, HTCC2506^T possessed XR and a complete gene set for AAnP together. A gene cluster encoding the AAnP apparatus was composed of bchIDO-crtCDF-bchCXYZ-pufBALMC-puhE-acsF-puhCBA-lhaA-bchMLHBNF-aerR-ppsR-ubiA-pucC-bchP-hemT. Mu-like prophage sequences were located closely adjacent to the AAnP gene cluster, which might imply the possibility of the lateral gene transfer of the AAnP gene cluster. The XR gene was followed by blh, a gene involved in retinal biosynthesis (16). To our knowledge, this is the first report of a microbe possessing both an AAnP apparatus and a rhodopsin family protein, although the two gene sets in HTCC2506^T had been separately reported to be present (5, 13). The HTCC2506^T genome also encoded a bacteriophytochrome (6, 7), a light-regulated signal transduction histidine kinase. Overall, the existence of a diverse repertoire of genes for sensing or harvesting of light energy implicates the importance of phototrophic metabolism for HTCC2506^T.In addition to genes for phototrophy, the genome contained several genes with diverse metabolic potential. A lithotrophic mode of energy acquisition was predicted from the presence of the form II coxSLM genes, which encode aerobic-type carbon monoxide dehydrogenase (9). As expected from the Mn(II)-oxidizing activity of HTCC2506^T, the genome also encoded a multicopper oxidase (MCO) enzyme, suggesting a potential lithotrophy. In terms of carbon assimilation, genes encoding RuBisCO and phosphoribulokinase of the Calvin-Benson-Bassham cycle (11) were predicted, suggesting the possibility of autotrophic CO₂ fixation in HTCC2506^T. Serine transhydroxymethylase for formaldehyde assimilation (12) was predicted. A gene encoding dimethylsulfoniopropionate (DMSP) lyase, which conveys the production of dimethylsulfide from DMSP (4), was also found in the genome.Although HTCC2506^T was originally isolated as a chemoheterotroph (2), the genome sequence clearly shows the phototrophic potential of this bacterium. This finding, combined with the prediction of many genes related to lithotrophy, carbon fixation, C₁ compound assimilation, and DMSP lysis, suggests that F. pelagi HTCC2506^T may use a wide range of potential metabolic functions to survive in the marine euphotic environment.