Identification of a thiosulfate utilization gene cluster from the green phototrophic bacterium Chlorobium limicola

Chlorobium is an autotrophic, green phototrophic bacterium which uses reduced sulfur compounds to fix carbon dioxide in the light. The pathways for the oxidation of sulfide, sulfur, and thiosulfate have not been characterized with certainty for any species of bacteria. However, soluble cytochrome c-551 and flavocytochrome c (FCSD) have previously been implicated in the oxidation of thiosulfate and sulfide on the basis of enzyme assays in Chlorobium. We have now made a number of observations relating to the oxidation of reduced sulfur compounds. (1) Western analysis shows that soluble cytochrome c-551 in Chlorobium limicola is regulated by thiosulfate, consistent with a role in the utilization of thiosulfate. (2) A membrane-bound flavocytochrome c-sulfide dehydrogenase (which is normally a soluble protein in other species) is constitutive and not regulated by sulfide as expected for an obligately autotrophic species dependent upon sulfide. (3) We have cloned the cytochrome c-551 gene from C. limicola and have found seven other genes, which are also presumably involved in sulfur metabolism and located near that for cytochrome c-551 (SoxA). These include genes for a flavocytochrome c flavoprotein homologue (SoxF2), a nucleotidase homologue (SoxB), four small proteins (including SoxX, SoxY, and SoxZ), and a thiol-disulfide interchange protein homologue (SoxW). (4) We have established that the constitutively expressed FCSD genes (soxEF1) are located elsewhere in the genome. (5) Through a database search, we have found that the eight thiosulfate utilization genes are clustered in the same order in the Chlorobium tepidum genome (www.tigr.org). Similar thiosulfate utilization gene clusters occur in at least six other bacterial species but may additionally include genes for rhodanese and sulfite dehydrogenase.     

Ecological significance of acetate assimilation by Chlorobium phaeobacteroides

Abstract The effect of different concentrations of sulfide and sulfur on the assimilation of acetate by Chlorobium phaeobacteroides was investigated in batch and continuous cultures.
In batch cultures the assimilation of acetate strictly depends on the initial concentration of sulfide. In continuous cultures the uptake of acetate depends not only on the reservoir concentration of sulfide but also on the dilution rate. The more severe the limitation of sulfide the higher the incorporation of acetate.
The very efficient uptake of acetate was also observed in batch cultures, but only immediately prior to sulfide depletion. After sulfide depletion, with sulfur still available, the uptake of acetate per mmol reducing power increased even further. This phenomenon, which has been overlooked since growth decreases drastically after sulfide depletion due to incapacity for assimilatory sulfate reduction is of ecological importance in the formation of blooms of brown Chlorobium species.     

Sulfide utilization by the photosynthetic bacterium Chlorobium phaeobacteroides

Sulfide and sulfur are used by the photosynthetic bacterium Chlorobium phaeobacteroides as electron donors. Sulfide and sulfur consumption was found to be affected by sulfide concentration in the medium. Raising the sulfide concentration from 0.28 mM to 5.05 mM caused an increase in the amount of S⁼ utilized per growth unit from 0.58 mM to 2.32 mM. This increase in sulfide utilization was not reflected in a higher photosynthetic activity. Sulfide and sulfur consumption was also influenced by light intensity, with higher light intensity sulfide consumption was increased. In Lake Kinneret, Chlorobium phaeobacteroides did not bloom in the thermocline layer until sulfide concentrations reached 0.03–0.06 mM.     

Microbial Recovery of Sulfur from Thiosulfate-Bearing Wastewater with Phototrophic and Sulfur-Reducing Bacteria

The spent caustic wastewater from the oxidation of sulfide present in offshore natural gas production mainly comprises thiosulfate and sulfate. A biocatalytic process, employing phototrophic green sulfur bacteria in symbiosis with sulfate-reducing bacteria, is described in this paper for the production of sulfur from the spent caustic wastewater, with synthetic wastewater as the model system. The process entails the conversion of thiosulfate to sulfur and sulfate by photosynthetic green sulfur bacteria Chlorobium vibrioforme f. thiosulfatophilum. Sulfate formed in turn is removed by Desulfovibrio desulfuricans to sulfide, which is further converted to sulfur by Chlorobium limicola through photooxidation. Sulfide is also oxidized to sulfur and sulfate via thiosulfate as an intermediate by Chlorobium vibrioforme f. thiosulfatophilum.     

Anoxygenic microbial mats of hot springs: thermophilic Chlorobium sp.

Abstract Non-laminated, green to yellow-green microbial mats, with Chlorobium sp. as the only phototroph, occurred from 55 to about 40°C in hot springs in and near Rotorua, New Zealand. The pH ranged from 4.3 to 6.2 and sulfide from 0.2 to 1.8 mM. This Chlorobium sp. is unique in its ability to form populations at temperatures as high as 55°C. Spectroradiometric measurements with a fiber-optic microprobe in the intact Chlorobium mass showed great opacity with less than 0.1% of the incident radiation (at photosynthetically usable wavelengths) available at 0.7 mm depth within the mat, although the concentrated Chlorium population sometimes extended to 3 mm depth. Sulfide-dependent, anoxygenic photosynthesis was demonstrated by [¹⁴C]bicarbonate assimilation in mat suspensions and in intact mats by a sulfide-specific microelectrode. No oxygen evolution occurred and no O₂ was present within the mat. A light-enhanced uptake of [¹⁴C]acetate also occurred in cell suspensions. This rate was not enhanced by sulfide.     

Susceptibility of various purple and green sulfur bacteria to different antimicrobial agents

Abstract Several purple and green sulfur bacteria (genera Chromatium, Thiocapsa and Chlorobium ) were tested for their sensitivity to different antimicrobial agents by a disc diffusion assay, using thioacetamide as a source of hydrogen sulfide for plate growth. Chlorobium limicola strains were more sensitive to amoxicillin, erythromycin and nalidixic acid, whereas gentamicin and netilmicin were more active against the purple bacteria tested. None of the organisms were sensitive to oxacillin and trimethoprim + sulfamethoxazole. The critical concentrations at the edge of the inhibition zone were also calculated for three organisms and the antimicrobials colistin, mitomycin C, penicillin G, rifampicin, and streptomycin. The results obtained suggest that colistin, mitomycin C, penicillin G would provide selective conditions against the growth of Chlorobium limicola strains, while streptomycin and other aminoglycoside antibiotics would select against purple bacteria.     

Coexistence of Chlorobium and Chromatium in a sulfide-limited continuous culture

Competition experiments between Chromatium vinosum and Chlorobium limicola in sulfide-limited continuous culture under photolithoautotrophic conditions resulted in the coexistence of both organisms. The ratio between the two bacteria was dilution-rate as well as pH dependent. The observed coexistence can be explained as a hitherto not reported form of dual substrate limitation. The two substrates involved are the electron donors sulfide (growth-limiting substrate in the reservoir vessel) and extracellular elemental sulfur (formed by Chlorobium as a result of sulfide oxidation). It is argued that, although Chlorobium may have the better affinity for both substrates involved, Chromatium can compete successfully on the basis of its intracellular storage of sulfur. Ecological implication of the observed coexistence with respect to natural blooms are discussed.     

Cytochromes of the green sulfur bacterium Chlorobium vibrioforme f. thiosulfatophilum. Purification,characterization and sulfur metabolism

Three cytochromes of the thiosulfate-utilizing green sulfur bacterium Chlorobium vibrioforme f. thiosulfatophilum were highly purified by ion exchange column chromatography and ammonium sulfate fractionation. All three cytochromes are located in the soluble fraction. Cytochrome c-551 (highest purity index obtained: A₂₈₀/A₄₁₆=0.39) shows maxima at 551 nm (-band), 521 nm (-band), and 416 nm (-band) for the reduced form. This cytochrome is an acidic protein with a molecular weight of 32,000, a redox potential of 150 mV, and an isoelectric point at pH 6.0. Cytochrome c-553 (highest purity index obtained: A₂₈₀/A₄₁₇=0.8) is also an acidic protein with maxima at 553,5 nm, 523,5 nm and 417 nm for the reduced form, a molecular weight of 63,000, a redox potential of 90 mV, an isoelectric point at pH 6.3, and it contains FAD as flavin component. It is autoxidizable and participates in sulfide oxidation, but cannot catalyze the reverse reaction. The cytochrome c-555 (highest purity index obtained: A₂₈₀/A₄₁₈=0.16) is a small basic protein with maxima at 555 nm, 523 nm and 418 nm (reduced form), a molecular weight of 12,500, an isoelectric point between pH 10 and 10.5, and a redox potential of 155 mV. The ratio of the cytochrome contents to each other is constant and does not change when the organism has only thiosulfate or sulfide as the main electron donor in the medium.The soluble fraction further contains the non-heme ironcontaining proteins rubredoxin and ferredoxin. The anaerobic sulfide oxidation in a growing culture of Chlorobium vibrioforme f. thiosulfatophilum is accompanied by a rapid formation of thiosulfate, which is only utilized when sulfide is no longer available, while the elemental sulfur concentration increases constantly until thiosulfate is consumed.Non-common abbreviations C Chlorobium - SDS sodium dodecylsulfate - HIPIP high-potential-iron-sulfur-protein     

Growth yields of green sulfur bacteria in mixed cultures with sulfur and sulfate reducing bacteria

1. Dry weight yields from mixed cultures ofProsthecochloris aestuarii orChlorobium limicola with the sulfur reducingDesulfuromonas acetoxidans were determined on different growth limiting amounts of acetate, ethanol or propanol. The obtained yields agreed well with values predicted from stoichiometric calculations. 2. From mixed cultures of twoChlorobium limicola strains withDesulfovibrio desulfuricans orD. gigas on ethanol as the growth limiting substrate, dry weight yields were obtained as calculated for the complete utilization of the ethanol by the mixed cultures. 3. Dry weight yield determinations for two pure cultures ofChlorobium limicola with different growth limiting amounts of sulfide in the absence and presence of excess acetate confirmed that acetate is incorporated byChlorobium in a fixed proportion to sulfide; compared to the yield in the absence of acetate the yield is increased two to threefold in the presence of acetate. 4. The lowest possible sulfide concentrations necessary for optimal growth of mixed cultures of eitherProsthecochloris orChlorobium withDesulfuromonas on acetate were 7–8 mg H₂S per liter of medium. 5. Doubling times at the growth rate limiting light intensities of 5, 10, 20, 50, 100 and 200 lux were determined under optimal growth conditions for the following phototrophic bacteria:Prosthecochloris aestuarii, Chlorobium phaeovibriodes, Chromatium vinosum andRhodopseudomonas capsulata. Reasonably good growth was still obtained withProsthecochloris at 10 and 5 lux light intensity at which no growth of the purple bacteria could be observed.     

Microbially — related redox changes in a subtropical lake I.In situ monitoring of the annual redox cycle

Using a recently developedin situ multiprobe the redox development in the water column of warm-monomictic Lake Kinneret was investigated during three annual cycles. During the time when sulfide release into the meta- and hypolimnion is initiated, our measurements show a linear relationship, close to the thermodynamic function, between the platinum electrode potential and the amount of sulfide produced by the sulfate reducing bacteria. A change of this relationship during summer stratification coincides with the bloom of the phototrophic sulfur bacteriumChlorobium phaeobacteroides.     

Green sulfur bacteria from hypersaline Chiprana Lake (Monegros,Spain): habitat description and phylogenetic relationship of isolated strains

The 'Salada de Chiprana' (Chiprana Lake) is a hypersaline (30-73 per thousand), permanent and shallow lake of endorheic origin in a semi-arid region of the Ebro depression (Aragon, Spain). Magnesium sulfate and sodium chloride represent the main salts of this athalassohaline environment. Anoxic conditions occurred periodically in the bottom layers of the lake during the study period. When stratified, high sulfide concentrations (up to 7 mM) were measured in the hypolimnion. Physical and chemical conditions gave rise to the development of very dense green sulfur bacteria blooms (10.7 mg l(-1) of BChl c and 16.7 mg l(-1) of BChl d) at 0.5-1 m from the bottom. Microscopic observations revealed that cells morphologically similar to Chlorobium vibrioforme were dominant in the phototrophic bacterial community, but Prosthecochloris aestuarii was also found sometimes at lower concentrations, as revealed by both microscopic observation and flow cytometric analyses. Deep agar dilution series allowed to obtain several axenic cultures of phototrophic bacteria. They were identified according to their morphology, pigment composition and phylogenetic relationships (16S rDNA sequence analysis). Two of the sequenced strains (CHP3401 and CHP3402) belonged to the green sulfur bacteria and were related to Prosthecochloris aestuarii SK413(T) and Chlorobium vibrioforme DSM260(T), respectively. HPLC analyses of both natural samples and Chlorobium vibrioforme isolates indicated that these strains contained both BChl c and BChl d. Phylogenetic results suggested that Chlorobium vibrioforme strains DSM260(T) and CHP3402, all sequenced strains of Prosthecochloris aestuarii and strain CIB2401 constitute a separate cluster of green sulfur bacteria, all of them isolated from marine to hypersaline habitats.     

In situ analysis of sulfur in the sulfur globules of phototrophic sulfur bacteria by X-ray absorption near edge spectroscopy.

During the oxidation of sulfide and thiosulfate purple and green sulfur bacteria accumulate globules of 'elemental' sulfur. Although essential for a thorough understanding of sulfur metabolism in these organisms, the exact chemical nature of the stored sulfur is still unclear. We applied sulfur K-edge X-ray absorption near edge spectroscopy (XANES) to probe the forms of sulfur in intact cells. Comparing XANES spectra of Allochromatium vinosum, Thiocapsa roseopersicina, Marichromatium purpuratum, Halorhodospira halophila and Chlorobium vibrioforme grown photolithoautotrophically on sulfide with reference probes (fingerprint method), we found sulfur chains with the structure R-S(n)-R. Evidence for the presence of sulfur rings, polythionates and anionic polysulfides in the sulfur globules of these bacteria was not obtained.     

Ciliates from a fresh water sulfuretum

Ciliates were collected from a freshwater sulfuretum, Lake Cisó, which is part of a gypsum karstic area whose main feature is Lake Banyoles (Girona, Spain). Chromatium, Lamprocystis and Chlorobium are the major phototrophic sulfur bacteria in Lake Cisó. Blooms of a photosynthetic cryptomonad (up to 5 X 10(5) ind ml-1) were found at the metalimnion. The community of ciliates could be divided in three groups: aerobic, cosmopolitan, genera such as Stentor and Vorticella, in the epilimnion; a large population (up to 10(4) ind ml-1) of Coleps, adapted to low concentrations of both oxygen and sulfide, together with a few individuals of the equally sulfide-tolerant genus Paramecium, in the metalimnion, and anaerobic, true sulfide-loving genera such as Plagiopyla and Metopus, in the hypolimnion, where sulfide concentration was between 0.6 and 1.2 mM.     

Thiosulfate sulfur transferases (Rhodaneses) ofChlorobium vibrioforme f.thiosulfatophilum

Two enzymes containing thiosulfate sulfur transferase activity were purified fromChlorobium vibrioforme f.thiosulfatophilum by ion exchange chromatography, gel filtration and isoelectrofocusing. Enzyme I is a basic protein with an isoelectric point at pH 9.2 and has a molecular weight of 39,000. TheK _m-values for thiosulfate and cyanide of the purified basic protein were 0.25 mM (thiosulfate) and 5 mM (cyanide). Enzyme II is an acidic protein. The enzyme has an isoelectric point at pH 4.6–4.7 and a molecular weight of 34,000. TheK _m-values of the acidic protein were found to be 5 mM for thiosulfate and 125 mM for cyanide.In addition to thiosulfate sulfur transferase activity, cellfree extracts ofChlorobium vibrioforme f.thiosulfatophilum also contained low thiosulfate oxidase activity and negligible thiosulfate reductase activity. The percent distribution of thiosulfate sulfur transferase and thiosulfate oxidase activities in the organism was independent of the offered sulfur compound (thiosulfate, sulfide or both) in the medium.Abbreviations C Chlorobium - SDS sodium dodecylsulfate Dedicated to Prof. Dr. Norbert Pfennig on the occasion of his 60th birthday     

34S/32S fractionation in sulfur cycles catalyzed by anaerobic bacteria.

Stable isotopic distributions in the sulfur cycle were studied with pure and mixed cultures of the anaerobic bacteria, Chlorobium vibrioforme and Desulfovibrio vulgaris. D. vulgaris and C. vibrioforme can catalyze three reactions constituting a complete anaerobic sulfur cycle: reduction of sulfate to sulfide (D. vulgaris), oxidation of sulfide to elemental sulfur (C. vibrioforme), and oxidation of sulfur to sulfate (C. vibrioforme). In all experiments, the first and last reactions favored concentration of the light 32S isotope in products (isotopic fractionation factor epsilon = -7.2 and -1.7%, respectively), whereas oxidation of sulfide favored concentration of the heavy 34S isotope in products (epsilon = +1.7%). Experimental results and model calculations suggest that elemental sulfur enriched in 34S versus sulfide may be a biogeochemical marker for the presence of sulfide-oxidizing bacteria in modern and ancient environments.     

Covalent structure of the diheme cytochrome subunit and amino-terminal sequence of the flavoprotein subunit of flavocytochrome c from Chromatium vinosum.

The complete sequence of the 21-kDa cytochrome subunit of the flavocytochrome c (FC) from the purple phototrophic bacterium Chromatium vinosum has been determined to be as follows: EPTAEMLTNNCAGCHG THGNSVGPASPSIAQMDPMVFVEVMEGFKSGEIAS TIMGRIAKGYSTADFEKMAGYFKQQTYQPAKQSF DTALADTGAKLHDKYCEKCHVEGGKPLADEEDY HILAGQWTPYLQYAMSDFREERRPMEKKMASKL RELLKAEGDAGLDALFAFYASQQ. The sequence is the first example of a diheme cytochrome in a flavocytochrome complex. Although the locations of the heme binding sites and the heme ligands suggest that the cytochrome subunit is the result of gene doubling of a type I cytochrome c, as found with Azotobacter cytochrome c4, the extremely low similarity of only 7% between the two halves of the Chromatium FC heme subunit rather suggests that gene fusion is at the evolutionary origin of this cytochrome. The two halves also require a single residue internal deletion for alignment. The first half of the Chromatium FC heme subunit is 39% similar to the monoheme subunit of the FC from the green phototrophic bacterium Chlorobium thiosulfatophilum, but the second half is only 9% similar to the Chlorobium subunit. The N-terminal sequence of the Chromatium FC flavin subunit was determined up to residue 41 as AGRKVVVVGGGTGGATAAKYIKLADPSIEVTLIEP NTKYYT. It shows more similarity to the Chlorobium FC flavin subunit (60%) than do the two heme subunits. The N terminus of the flavin subunit is homologous to a number of flavoproteins, including succinate dehydrogenase, glutathione reductase, and monamine oxidase. There is no obvious homology to the Pseudomonas putida FC flavin subunit, which suggests that the two types of flavocytochrome c arose by convergent evolution. This is consistent with the dissimilar enzyme activities of FC as sulfide dehydrogenase in the phototrophic bacteria and as p-cresol methylhydroxylase in Pseudomonas. We also present a sequence "fingerprint" pattern for the recognition of FAD-binding proteins which is an extended version of the consensus sequence previously presented (Wierenga, R. K., Terpstra, P., and Hol, W. G. J. (1986) J. Mol. Biol. 187, 101-107) for nucleotide binding sites.     

34S/32S fractionation in sulfur cycles catalyzed by anaerobic bacteria

Stable isotopic distributions in the sulfur cycle were studied with pure and mixed cultures of the anaerobic bacteria, Chlorobium vibrioforme and Desulfovibrio vulgaris. D. vulgaris and C. vibrioforme can catalyze three reactions constituting a complete anaerobic sulfur cycle: reduction of sulfate to sulfide (D. vulgaris), oxidation of sulfide to elemental sulfur (C. vibrioforme), and oxidation of sulfur to sulfate (C. vibrioforme). In all experiments, the first and last reactions favored concentration of the light 32S isotope in products (isotopic fractionation factor epsilon = -7.2 and -1.7%, respectively), whereas oxidation of sulfide favored concentration of the heavy 34S isotope in products (epsilon = +1.7%). Experimental results and model calculations suggest that elemental sulfur enriched in 34S versus sulfide may be a biogeochemical marker for the presence of sulfide-oxidizing bacteria in modern and ancient environments.     

Factors determining annual changes in bacterial photosynthetic pigments in holomictic lake cisó, Spain

The pigments and biomass of anoxygenic phototrophic bacteria were measured during a year cycle in Lake Cisó (Girona, Spain). Two genera, Chromatium and Chlorobium, accounted for most of the bacterial population. The bacteria were present throughout the year despite complete mixing of the lake during fall and winter. This was possible because the sulfide production in the sediment was high enough to make the lake anaerobic to the very surface. Solar radiation, temperature, and biomass of Chromatium sp. were found to be important in determining pigment concentrations by correlation analysis. Sulfide concentration and biomass of Chlorobium spp. were found to be unimportant. A path analysis was performed to determine what percentage of the variability of pigments could be explained by the variables studied. Since a high percentage could be explained, it was possible to conclude that solar radiation, temperature, and biomass of Chromatium sp. were the main variables.     

Ecophysiological properties of photosynthesizing bacteria from the Black Sea chemocline zone

In May 1998, during the fifty-first voyage on board the research vessel Professor Vodyanitskii, a comparative study was conducted of the species diversity of green and purple sulfur bacteria in the water column of the chemocline zone at deep-sea stations and on the bottom surface of the Black Sea shallow regions. At three deep-sea stations, the accumulation of photosynthesizing bacteria in the chemocline zone at a depth of 85-115 m was revealed on the basis of the distribution of potential values of carbon dioxide light fixation. The location of the site of potential carbon dioxide light fixation suggests that the photosynthesis may be determined by the activity of the brown Chlorobium sp., revealed earlier at these depths. Enrichment cultures of brown sulfur bacteria were obtained from samples taken at the deep-sea stations. By morphology, these bacteria, assigned to Chlorobium sp., appear as nonmotile straight or slightly curved rods 0.3-0.5 x 0.7-1.2 microm in size; sometimes, they form short chains. Ultrathin sections show photosynthesizing antenna-like structures, chlorosomes, typical of Chlorobiaceae. The cultures depended on the presence of NaCl (20 g/l) for growth, which corresponds to the mineralization of Black Sea water. The bacteria could grow photoautotrophically, utilizing sulfide, but the Black Sea strains grew much more slowly than the known species of brown sulfur bacteria isolated from saline or freshwater meromictic lakes. The best growth of the strains studied in this work occurred in media containing ethanol (0.5 g) or sodium acetate (1 g/l) and low amounts of sulfide (0.4 mM), which is consistent with the conditions of syntrophic growth with sulfidogens. The data obtained allow us to conclude that the cultures of brown sulfur bacteria are especially adapted to developing at large depths under conditions of electron donor deficiency owing to syntrophic development with sulfate reducers. The species composition of the photosynthetic bacteria developing in the bottom sediments of shallow stations differed substantially from that observed at deep-sea stations. Pure cultures of the green Chlorobium sp. BS 1C and BS 2C (chlorobactin as the carotenoid), purple sulfur bacteria Chromatium sp. BS 1Ch (containing spirilloxanthine series pigments), and Thiocapsa marina BS 2Tc (containing the carotenoid okenone) were obtained from samples of sediments at shallow-water stations. Brown sulfur bacteria were absent in the sediment samples obtained from the Black Sea shallow-water stations 1 and 2.     

A thermophilic green sulfur bacterium from New Zealand hot springs,Chlorobium tepidum sp. nov.

Thermophilic green sulfur bacteria of the genus Chlorobium were isolated from certain acidic high sulfide New Zealand hot springs. Cells were Gram-negative nonmotile rods of variable length and contained bacteriochlorophyll c and chlorosomes. Cultures of thermophilic chlorobia grew only under anaerobic, phototrophic conditions, either photoautotrophically or photoheterotrophically. The optimum growth temperature for the strains of thermophilic green sulfur bacteria isolated was 47–48°C with generation times of about 2 h being observed. The upper temperature limit for growth was about 52°C. Thiosulfate was a major electron donor for photoautotrophic growth while sulfide alone was only poorly used. N₂ fixation was observed at 48°C and cell suspensions readily reduced acetylene to ethylene. The G+C content of DNA from strains of thermophilic chlorobia was 56.5–58.2 mol% and the organisms positioned phylogenetically within the green sulfur bacterial branch of the domain Bacteria. The new phototrophs are described as a new species of the genus Chlorobium, Chlorobium tepidum.This paper is dedicated to Professor Norbert Pfennig on the occasion of his 65th birthday