Phototrophic Sulfide Oxidation Research Articles

Anoxygenic photosynthesis and iron-sulfur metabolic potential of Chlorobia populations from seasonally anoxic Boreal Shield lakes.

Aquatic environments with high levels of dissolved ferrous iron and low levels of sulfate serve as an important systems for exploring biogeochemical processes relevant to the early Earth. Boreal Shield lakes, which number in the tens of millions globally, commonly develop seasonally anoxic waters that become iron rich and sulfate poor, yet the iron-sulfur microbiology of these systems has been poorly examined. Here we use genome-resolved metagenomics and enrichment cultivation to explore the metabolic diversity and ecology of anoxygenic photosynthesis and iron/sulfur cycling in the anoxic water columns of three Boreal Shield lakes. We recovered four high-completeness and low-contamination draft genome bins assigned to the class Chlorobia (formerly phylum Chlorobi) from environmental metagenome data and enriched two novel sulfide-oxidizing species, also from the Chlorobia. The sequenced genomes of both enriched species, including the novel "Candidatus Chlorobium canadense", encoded the cyc2 gene that is associated with photoferrotrophy among cultured Chlorobia members, along with genes for phototrophic sulfide oxidation. One environmental genome bin also encoded cyc2. Despite the presence of cyc2 in the corresponding draft genome, we were unable to induce photoferrotrophy in "Ca. Chlorobium canadense". Genomic potential for phototrophic sulfide oxidation was more commonly detected than cyc2 among environmental genome bins of Chlorobia, and metagenome and cultivation data suggested the potential for cryptic sulfur cycling to fuel sulfide-based growth. Overall, our results provide an important basis for further probing the functional role of cyc2 and indicate that anoxygenic photoautotrophs in Boreal Shield lakes could have underexplored photophysiology pertinent to understanding Earth's early microbial communities.

Diurnal variations in sulfur transformations at the chemocline of a stratified freshwater lake

In order to characterize biogeochemical sulfur cycling in the metalimnion of a thermally stratified freshwater lake, we followed changes in the concentrations and isotopic composition of sulfur species during a 24-h period, during which the chemocline oscillated at an amplitude of 5.3 m due to internal wave activity. Hourly sampling at a fixed depth (17.1 m) enabled study of redox changes during the transition from oxic to sulfidic conditions and vice versa. The oxidation–reduction potential, pH, conductivity and turbidity correlated linearly with the water temperature (a proxy for depth relative to the chemocline). The highest concentrations of thiosulfate and sulfite were detected approximately 2.5 m below the chemocline. Concentrations of zero-valent sulfur increased ~ 10 fold when the chemocline rose into the photic zone due to phototrophic sulfide oxidation. Triple isotopic composition of sulfur species indicates a shift with depth from values typical for sulfate reduction right below the chemocline to values which may be explained by either sulfate reduction alone or by a combination of microbial sulfate reduction and microbial sulfate disproportionation. We conclude that consumption of hydrogen sulfide at the chemocline of Lake Kinneret is controlled by the combination of its chemical and/or chemotrophic oxidation to sulfur oxoanions and predominantly phototrophic oxidation to zero-valent sulfur.

Dark aerobic sulfide oxidation by anoxygenic phototrophs in anoxic waters.

Anoxygenic phototrophic sulfide oxidation by green and purple sulfur bacteria (PSB) plays a key role in sulfide removal from anoxic shallow sediments and stratified waters. Although some PSB can also oxidize sulfide with nitrate and oxygen, little is known about the prevalence of this chemolithotrophic lifestyle in the environment. In this study, we investigated the role of these phototrophs in light-independent sulfide removal in the chemocline of Lake Cadagno. Our temporally resolved, high-resolution chemical profiles indicated that dark sulfide oxidation was coupled to high oxygen consumption rates of ~9 μM O2 ·h-1 . Single-cell analyses of lake water incubated with 13 CO2 in the dark revealed that Chromatium okenii was to a large extent responsible for aerobic sulfide oxidation and it accounted for up to 40% of total dark carbon fixation. The genome of Chr. okenii reconstructed from the Lake Cadagno metagenome confirms its capacity for microaerophilic growth and provides further insights into its metabolic capabilities. Moreover, our genomic and single-cell data indicated that other PSB grow microaerobically in these apparently anoxic waters. Altogether, our observations suggest that aerobic respiration may not only play an underappreciated role in anoxic environments but also that organisms typically considered strict anaerobes may be involved.

Large-scale microalgal biomass production for hydrothermal liquefaction – petroleum refinery approach

Sulfide oxidation forms a critical step in the global sulfur cycle, although this process is notoriously difficult to constrain due to the multiple pathways and highly reactive intermediates involved. Multiple sulfur isotopes (δ34S and Δ33S) can provide a powerful tool for unravelling sulfur cycling processes in modern (and ancient) environments, although they have had limited application to systems with well-resolved oxidative S cycling. In this study, we report the major (δ34S) and minor (Δ33S) isotope values of sulfur compounds in streams and sediments from the sulfidic Frasassi cave system, Marche Region, Italy. These microaerophilic cave streams host prominent white biofilms dominated by chemolithotrophic organisms that oxidize sulfide to S0, allowing us to estimate S isotope fractionations associated with in situ sulfide oxidation and to evaluate any resulting isotope biosignatures. Our results demonstrate that chemolithotrophic sulfide oxidation produces 34S enrichments in the S0 products that are larger than those previously measured in laboratory experiments, with 34εS0–H2S of up to 8‰ calculated. These small reverse isotope effects are similar to those produced during phototrophic sulfide oxidation (⩽7‰), but distinct from the small normal isotope effects previously calculated for abiotic oxidation of sulfide with O2 (∼−5‰). An inverse correlation between the magnitude of 34εS0–H2S effects and sulfide availability, along with substantial differences in Δ33S, both support complex sulfide oxidation pathways and intracellular recycling of S intermediates by organisms inhabiting the biofilms. At the ecosystem level, we calculate fractionations of less than 40‰ between sulfide and sulfate in the water column and in the sediments. These fractionations are smaller than those typically calculated for systems dominated by sulfate reduction (>50‰), and contrast with the commonly held assumption that oxidative recycling of sulfide generally increases overall fractionations. The relatively small fractionations appear to be related to the sequestration of S0 in the biofilms (either intra- or extra-cellularly), which removes this intermediate substrate from fractionation by further disproportionation or oxidation reactions. In addition, the net 33λH2S–SO4 values calculated in this system are larger than data published for systems dominated by reductive sulfur cycling, partially due to the isotopic imprint of chemolithotrophic sulfide oxidation on the aqueous sulfide pool. These distinct isotopic relationships are retained in the sedimentary sulfur pool, suggesting that trends in 34S and 33S values could provide an isotopic fingerprint of such chemolithotrophic ecosystems in modern and ancient environments.

A model of phototrophic sulfide oxidation in a stratified estuary

AbstractSulfide accumulated as a result of microbial sulfate reduction in sediments and the bottom waters of stratified systems can be re‐oxidized via an array of biotic and abiotic reactions. A one‐dimensional diffusion‐reaction model was developed and applied to 4 yr of physical and chemical data from the stratified water column of the Chesapeake Bay in order to quantify the impact of different sulfide oxidation processes at the redox interface during slack tide. This dataset and the model simulations highlight short‐term and interannual variation in the physical structure and the distribution of key redox species (O2, H2S, S0, Fe2+, Mn2+, FeOOH, MnO2) throughout the water column. The model evaluates links between oxygen, sulfur, iron and manganese cycling, and includes the novel consideration of sulfide oxidation by phototrophic sulfide oxidizing bacteria (PSOB), which are a common component of the Bay. Model simulations demonstrate that phototrophic sulfide oxidation can account for up to 58% of total sulfide oxidation, depending upon the depth of the oxic/anoxic interface. The results of this study yield an approach to parameterizing PSOB activity, and quantify the variable role that PSOB play in sulfide oxidation in the Chesapeake Bay as redox conditions in the water column change, which has applications for both modern and ancient environments.

A comprehensive sulfur and oxygen isotope study of sulfur cycling in a shallow, hyper-euxinic meromictic lake

Mahoney Lake is a permanently anoxic and sulfidic (euxinic) lake that has a dense plate of purple sulfur bacteria positioned at mid-water depth (∼7m) where free sulfide intercepts the photic zone. We analyzed the isotopic composition of sulfate (δ34SSO4 and δ18OSO4), sulfide (δ34SH2S), and the water (δ18OH2O) to track the potentially coupled processes of dissimilatory sulfate reduction and phototrophic sulfide oxidation within an aquatic environment with extremely high sulfide concentrations (>30mM). Large isotopic offsets observed between sulfate and sulfide within the monimolimnion (δ34SSO4-H2S=51‰) and within pore waters along the oxic margin (δ34SSO4-H2S>50‰) are consistent with sulfate reduction in both the sediments and the anoxic water column. Given the high sulfide concentrations of the lake, sulfur disproportionation is likely inoperable or limited to a very narrow zone in the chemocline, and therefore the large instantaneous fractionations are best explained by the microbial process of sulfate reduction. Pyrite extracted from the sediments reflects the isotopic composition of water column sulfide, suggesting that pyrite buried in the euxinic depocenter of the lake formed in the water column. The offset between sulfate and dissolved sulfide decreases at the chemocline (δ34SSO4-H2S=37‰), a trend possibly explained by elevated sulfate reduction rates and inconsistent with appreciable disproportionation within this interval. Water column sulfate exhibits a linear response in δ18OSO4–δ34SSO4 and the slope of this relationship suggests relatively high sulfate reduction rates that appear to respond to seasonal changes in the productivity of purple sulfur bacteria. Although photosynthetic activity within the microbial plate influences the δ18OSO4–δ34SSO4 relationship, the biosignature for photosynthetic sulfur bacteria is restricted to the oxic/anoxic transition zone and is apparently minor relative to the more prevalent process of sulfate reduction operative throughout the light-deprived deeper anoxic water column and sediment pore waters.

Sulfur isotope values in the sulfidic Frasassi cave system, central Italy: A case study of a chemolithotrophic S-based ecosystem

Sulfide oxidation forms a critical step in the global sulfur cycle, although this process is notoriously difficult to constrain due to the multiple pathways and highly reactive intermediates involved. Multiple sulfur isotopes (δ34S and Δ33S) can provide a powerful tool for unravelling sulfur cycling processes in modern (and ancient) environments, although they have had limited application to systems with well-resolved oxidative S cycling. In this study, we report the major (δ34S) and minor (Δ33S) isotope values of sulfur compounds in streams and sediments from the sulfidic Frasassi cave system, Marche Region, Italy. These microaerophilic cave streams host prominent white biofilms dominated by chemolithotrophic organisms that oxidize sulfide to S0, allowing us to estimate S isotope fractionations associated with in situ sulfide oxidation and to evaluate any resulting isotope biosignatures. Our results demonstrate that chemolithotrophic sulfide oxidation produces 34S enrichments in the S0 products that are larger than those previously measured in laboratory experiments, with 34εS0–H2S of up to 8‰ calculated. These small reverse isotope effects are similar to those produced during phototrophic sulfide oxidation (⩽7‰), but distinct from the small normal isotope effects previously calculated for abiotic oxidation of sulfide with O2 (∼−5‰). An inverse correlation between the magnitude of 34εS0–H2S effects and sulfide availability, along with substantial differences in Δ33S, both support complex sulfide oxidation pathways and intracellular recycling of S intermediates by organisms inhabiting the biofilms. At the ecosystem level, we calculate fractionations of less than 40‰ between sulfide and sulfate in the water column and in the sediments. These fractionations are smaller than those typically calculated for systems dominated by sulfate reduction (>50‰), and contrast with the commonly held assumption that oxidative recycling of sulfide generally increases overall fractionations. The relatively small fractionations appear to be related to the sequestration of S0 in the biofilms (either intra- or extra-cellularly), which removes this intermediate substrate from fractionation by further disproportionation or oxidation reactions. In addition, the net 33λH2S–SO4 values calculated in this system are larger than data published for systems dominated by reductive sulfur cycling, partially due to the isotopic imprint of chemolithotrophic sulfide oxidation on the aqueous sulfide pool. These distinct isotopic relationships are retained in the sedimentary sulfur pool, suggesting that trends in 34S and 33S values could provide an isotopic fingerprint of such chemolithotrophic ecosystems in modern and ancient environments.

Phototrophic sulfide oxidation: environmental insights and a method for kinetic analysis

Previously, we presented data that indicated microbial sulfide oxidation would out-compete strictly chemical, abiotic sulfide oxidation reactions under nearly all conditions relevant to extant ecosystems (Luther et al., 2011). In particular, we showed how anaerobic microbial sulfide oxidation rates were several orders of magnitude higher than even metal catalyzed aerobic sulfide oxidation processes. The fact that biotic anaerobic sulfide oxidation is kinetically superior to abiotic reactions implies that nearly all anaerobic and sulfidic environments should host microbial populations that oxidize sulfide at appreciable rates. This was likely an important biogeochemical process during long stretches of euxinia in the oceans suggested by the geologic record. In particular, phototrophic sulfide oxidation allows the utilization of carbon dioxide as the electron acceptor suggesting that this process should be particularly widespread rather than relying on the presence of other chemical oxidants. Using the Chesapeake Bay as an example, we argue that phototrophic sulfide oxidation may be more important in many environments than is currently appreciated. Finally, we present methodological considerations to assist other groups that wish to study this process.

Seasonal change in microbial sulfur cycling in monomictic Lake Fukami‐ike, Japan

Sulfur budgets and seasonal progression of sulfur cycling processes were investigated in Lake Fukami‐ike, a small monomictic lake in Japan. The sulfur isotopic mass balance shows that the main sulfur source is groundwater inflow (δ34S = ‐15.0‰). The sulfate influx is approximately 20% reduced by microbial sulfate reduction and deposited as sulfide (δ34S = ‐22.2‰; 34 kmol yr−1); the remaining exits from the outflow channel (δ34S = ‐12.6‰). In the water column, microbiological analyses reveal that green sulfur bacteria dominate more than 90% of the population in the anoxic layer. A monthly decrease in sulfate concentration at each depth indicates that sulfate reduction proceeds within the water column as a first‐order reaction because of low sulfate concentration (< 600 µmol L−1). The isotopic fractionation factor of sulfate reduction is estimated to be 0.980 by the isotopic and concentration data of sulfate and sulfide from April to August. Numerical simulation indicates that the relative contribution of phototrophic sulfide oxidation is over 50 times slower than sulfate reduction from April to August but over two times higher from October to November because of lower sulfate conditions (< 300 µmol L−1). Sulfate concentration is the factor for controlling the relative contribution of sulfate reduction and phototrophic sulfide oxidation in monomictic lakes, which contrasts with that observed in permanently stratified lakes.

Molecular ecology of a facultative swine waste lagoon

To investigate the microbial ecology of three facultative swine waste lagoons. Phylogenetic analysis of sequences in a 16S rRNA gene clone library and fluorescence in situ hybridization (FISH) analyses were used to assess bacterial diversity in a swine waste lagoon. FISH analysis and Gram-staining were used to compare the microbial communities of all three swine waste lagoons. Six operational taxonomic units were in high relative abundance and corresponded to the following phylotypes; Thiolamprovum, Verrucomicrobia, Acholeplasma, Turicibacter, Clostridium and Bacteroides. PCR was employed to detect the genes apsA and dsrAB which encode for enzymes specifically associated with dissimilatory sulfate-reduction within sulfate-reducing bacteria (SRB). Amplification of these genes confirmed their presence within the lagoons. All lagoons were dominated by purple sulfur bacteria, affiliated to Thiolamprovum pedioforme. The molecular identification of fermentative bacteria and SRB indicate the following metabolic processes within such facultative ponds: sulfur-cycling, fermentation, inter-species hydrogen transfer and carbon cycling. This study provides the first molecular evidence for the existence of a sulfur cycle which is linked to phototrophic sulfide oxidation by purple bacteria and organotrophic sulfate-reduction by SRB.

Barite deposition resulting from phototrophic sulfide-oxidizing bacterial activity

Barite (BaSO 4) deposits generally arise from mixing of soluble barium-containing fluids with sulfate-rich fluids. While the role of biological processes in modulating barium solubility has been shown, no studies have shown that the biological oxidation of sulfide to sulfate leads to barite deposition. Here we present an example of microbially mediated barite deposition in a continental setting. A spring in the Anadarko Basin of southwestern Oklahoma produces water containing abundant barium and sulfide. As emergent water travels down a stream to a nearby creek, sulfate concentration increases from 0.06 mM to 2.2 mM while Ba 2+ concentration drops from 0.4 mM to less than 7 μM. Stable isotope analysis, microbial activity studies, and in situ experiments provide evidence that as sulfide-rich water flows down the stream, anaerobic, anoxygenic, phototrophic bacteria play a dominant role in oxidizing sulfide to sulfate. Sulfate then precipitates with Ba 2+ producing barite as travertine, cements, crusts, and accumulations on microbial mats. Our studies suggest that phototrophic sulfide oxidation and concomitant sulfur cycling could prove to be important processes regulating the cycling of barium in continental sulfur-containing systems.

Molecular organic tracers of biogeochemical processes in a saline meromictic lake (Ace Lake)

The chemical structures, distribution and stable carbon isotopic compositions of lipids in a sediment core taken in meromictic Ace Lake (Antarctica) were analyzed to trace past biogeochemical cycling. Biomarkers from methanogenic archaea, methanotrophic bacteria and photosynthetic green sulfur bacteria were unambiguously assigned using organic geochemical understanding and by reference to what is known about the lake’s present-day ecosystem. For instance, saturated and unsaturated 2,6,10,15,19-pentamethylicosane, archaeol and sn2-hydroxyarchaeol were derived from methanogenic archaea. Carotenoid analysis revealed chlorobactene and isorenieratene derived from the green-colored and brown-colored strains of the green sulfur bacteria (Chlorobiaceae); isotopic analyses showed that they were 13C-enriched. Phytenes appear to be derived from photoautotrophs that use the Calvin-Benson cycle, while phytane has a different source, possibly within the archaea. The most 13C-depleted compounds (ca. −55‰) identified were 4-methyl-5α-cholest-8(14)-en-3β-ol, identified using an authentic standard, and co-occurring 4-methylsteradienes: these originate from the aerobic methanotrophic bacterium Methylosphaera hansonii. Lipids of photoautotrophic origin, steranes and alkenones, are relatively depleted (ca. −28 to −36‰) whilst archaeal biomarkers are relatively enriched in 13C (ca. −17 to −25‰). The structural and carbon isotope details of sedimentary lipids thus revealed aspects of in situ biogeochemical processes such as methane generation and oxidation and phototrophic sulfide oxidation.