Green Sulfur Bacteria Research Articles

Modulation of the chlorophyll singlet state by protein environment is a key aspect of photosynthesis and light-harvesting in biological systems. This modulation affects excited-state dynamics, energy transfer efficiency, and photochemical reactivity. The PscB subunit of the reaction center (RC) of green sulfur bacterium Cba. tepidum contains an iron-sulfur cluster domain that is involved in light-driven electron transfer and a domain of intrinsically disordered region. The latter seemingly coil around one of the two trimeric FMO in the FMO-RC, acting as a molecular clamp. In this work, spectroscopic comparative studies of FMO-only and FMO-PscB complexes were performed. Our study reveals that reconstitution of the PscB with FMO protein alters the spectral line shape of the excitonic band of BChl a manifold and the properties of its singlet excited state as state lifetime. Though not substantial, the observable altered 815-nm excitonic band suggests that clamping of PscB around trimeric FMO shell slightly affects the overall pigment packing network. Further application of time-resolved fluorescence and absorption suggested that reconstitution of FMO trimers with PscB at the excess molecular ratio of the latter one likely leads to spontaneous oligomerization of the pigmented FMO with enhanced quenching capabilities which are essentially required during PscB's recruiting of FMO trimers and sandwiching them between chlorosome and the membrane-embedded RCs.

Abstract Bacteriochlorophylls (BChls) c and e are responsible for the main part of the light-harvesting process in chlorosome antenna systems of green sulfur bacteria, and contain a methyl group at the peripheral C-20 position of their core chlorin rings. This study performed in vitro and in vivo analysis of the C-20 methyltransferase BchU derived from the green sulfur bacterium Chlorobaculum tepidum, which synthesizes BChl c, to clarify the role of this enzyme in the biosynthetic pathway. Although the reaction step of BchU in the biosynthesis could not be determined by genetic analysis, enzymatic assays using various substrates showed that BchU reacts primarily with substrates after hydration of BchF and BchV at the C-3 position. The results in this study allow the proposition of a biosynthetic pathway for BChl c and e involving this enzyme.

Abstract Microbial processes regulating carbon cycling in ancient oceans remain poorly understood, yet characterizing these processes is critical for understanding early Earth biogeochemistry. Here, we investigate microbial communities associated with sinking particles regulating carbon cycling in meromictic Fayetteville Green Lake, a mid‐Proterozoic marginal ocean analog. The lake's photic zone spans oxic through sulfidic conditions, where prokaryotic photoautotrophs contribute to sinking fluxes and organotrophs mediate remineralization across redox and irradiance gradients. To characterize microbial communities in the sinking flux over time and redox condition, we sequenced 16S rRNA amplicons recovered from sediment traps throughout the lake's water column over the course of an annual photoautotroph bloom. Purple sulfur bacteria dominated deep fluxes, while cyanobacteria and green sulfur bacteria contributed variably across depths but were more abundant in suspended communities. As the bloom waned, chemoautotrophic Epsilonbacteraeota gained dominance in deeper fluxes, possibly due to niche partitioning. The shallow flux was remineralized by microbes exposed to temporally fluctuating biogeochemical conditions. Putative temporal changes in the availability and quality of organic matter and terminal electron acceptors thus promoted a succession of low‐diversity communities with few dominant hydrolytic and acidogenic clades. Unchanging conditions at depth promoted higher diversity microbial communities with niches for specialists dominated by sulfur‐metabolizing and fermentative clades. These findings improve our understanding of carbon cycling in the ancient ocean and offer insights into future shifts under climate change and meromixis in lakes.

ABSTRACTThe late Palaeocene climate cooling event has been reported in the organic‐rich sediments of the second member of the Funing Formation (E1f2) in the Subei Basin. However, there is a lack of in‐depth research on the constraints of paleoclimate changes on paleoenvironment and biological sources that remain unclear. This study presents detailed molecular geochemical analyses from the lacustrine mudstones of the E1f2 in the Subei Basin. The proxies of paleosalinity (gammacerane/C30 hopane, β‐carotene/n‐C20 and extended tricyclic terpane ratio) and redox conditions (pristane/phytane, phytane/n‐C18 and dibenzothiophene/phenanthrene) suggest climate cooling enhanced a higher salinity and anoxic (ferruginous) water column during the lower unit of the E1f2 deposition. As the climate shifted to warmer and more humid conditions, water salinity and reducing conditions noticeably decreased. Proxies for biological source (maximum n‐alkane, C27/C29 sterane, 4‐methylsterane/C29 regular sterane and steranes/hopanes) indicate that cooling climate constrained biodiversity. A transition is observed from the dominance of halophilic algae in the lower unit to a bloom of phytoplankton and prokaryotes in the upper unit. In addition, high abundance aryl isoprenoids and heavy organic carbon isotope compositions suggest the occurrence of photic zone anoxia in the lower unit, potentially providing a new case of green sulphur bacteria that thrived in a ferruginous lacustrine environment. Our research provides perspectives for the evolution of watermass conditions and biological sources in the Subei Basin during the late Palaeocene, highlighting the important role of climate changes in the evolution of lacustrine environment conditions.

Two-dimensional electronic spectroscopy (2DES) is a powerful tool for exploring quantum effects in energy transport within photosynthetic systems and investigating novel material properties. However, simulating the dynamics of these experiments poses significant challenges for classical computers due to the large system sizes, long timescales, and numerous experiment repetitions involved. This paper introduces the probe qubit protocol (PQP)-for quantum simulation of 2DES on quantum devices-addressing these challenges. The PQP offers several enhancements over standard methods, notably reducing computational resources, by requiring only a single-qubit measurement per circuit run and achieving Heisenberg scaling in detection frequency resolution, without the need to apply expensive controlled evolution operators in the quantum circuit. The implementation of the PQP protocol requires only one additional ancilla qubit, the probe qubit, with one-to-all connectivity and two-qubit interactions between each system and probe qubits. We evaluate the computational resources necessary for this protocol in detail, demonstrating its function as a dynamic frequency-filtering method through numerical simulations. We find that simulations of the PQP on classical and quantum computers enable a reduction on the number of measurements, i.e., simulation runtime, and memory savings of several orders of magnitude relative to standard quantum simulation protocols of 2DES. The paper discusses the applicability of the PQP on near-term quantum devices and highlights potential applications where this spectroscopy simulation protocol could provide significant speedups over standard approaches such as the quantum simulation of 2DES applied to the Fenna-Matthews-Olson (FMO) complex in green sulfur bacteria.

In this study, the triplet-state properties of BChl a in the Fenna-Matthews-Olson (FMO) light-harvesting complex were interrogated in the absence and presence of PscB, a subunit of the Cba. tepidum reaction center (RC), at room temperature and at 77 K. Application of nanosecond time-resolved transient absorption spectroscopy supports a model in which the pathway of the triplet excitation decay within FMO has two phases, with a fast lifetime of 2.58 μs (0.57 μs at 77 K) and a slow lifetime of 44.8 μs (44.1 μs at 77 K) in the FMO-only sample. Reconstitution of PscB and FMO, however, alters the spectral signatures of BChl a excitons uniquely at 815 nm in the steady-state spectrum at 77 K. Additionally, the triplet-state lifetime of BChl a in the FMO-PscB complex shortens by almost 40% to 28.1 μs at 77 K. The two FMO trimers asymmetrically interfacing with the homodimeric RC wire excitation energy from the chlorosome to the latter. Our data supports that the single central PscB, besides its redox active roles as the electron mediators to ferredoxin, is highly plausibly involved in fine-tuning the asymmetric excitation energy transfer from two branches of FMO to the RC in green sulfur bacteria.

BackgroundMeromictic lakes, with their stratified water columns, are modern analogs for ancient euxinic (anoxic and sulfidic) oceans, where anaerobic sulfur-oxidizing purple and green sulfur bacteria (PSB and GSB) dominated as primary producers. Recent studies suggest a potential role of viruses in the metabolisms and biosignatures of these bacteria, but conclusive evidence of viral replication and activity in such lakes is still lacking.ResultsHere, we investigate viral activity in the upper mixed layer (mixolimnion), the anoxic bottom (monimolimnion), and the microbial plate (a dense layer of phototrophic sulfur bacteria forming at the boundary between the oxygenated mixolimnion and the anoxic monimolimnion) of three meromictic lakes: Poison and Lime Blue Lakes (WA, USA) and Mahoney Lake (BC, CA). Geochemical profiles of two lakes, Mahoney and Poison, which are dominated by PSB, show a sharp chemocline, whereas Lime Blue displays a less steep chemical gradient and hosts a mixture of PSB and GSB. Viral gene transcription and epifluorescence microscopy revealed depth-dependent patterns in viral activity. The two strongly stratified, PSB-dominated lakes showed a significant decrease in the virus-to-microbe ratio (VMR) in their microbial plates, suggesting reduced viral particle production via lysis. Metatranscriptome data corroborated this trend by showing lower levels of viral gene expression in these microbial plates, higher expression of CRISPR defense and lysogeny-related genes, and relatively high expression of photosynthesis-related viral genes. Conversely, the third lake, which harbors a mix of PSB and GSB, exhibited low microbial density, high VMR, and high viral transcriptional activity. Viral transcription levels significantly correlated with VMR in the microbial plates and bottom layers, but this relationship was absent in low-density, oxic surface samples.ConclusionsHere, two independent lines of evidence, abundances and gene expression, show reduced viral lytic production in microbial plates dominated by PSB in stratified lakes. This suggests that viral lysis may contribute less to bacterial community structuring in these high-density microbial plates. Rather, other viral-mediated mechanisms, such as lysogeny and the expression of auxiliary metabolic genes, may represent a more significant viral influence on bacterial physiology and geochemistry. These patterns in virus-bacteria interactions may be consequential for the interpretations of biosignatures left by these bacterial groups in the geologic record.164hab4UvHT36hzXXdav9cVideo

Lake Cadagno is a meromictic alpine lake characterized by permanent stratification, which creates a permanent anoxic environment that supports the growth of anoxygenic phototrophic sulfur bacteria. The seasonality and interseasonality of these microorganisms were examined over a three-year period (2019–2021) through regular monitoring of the water column. A variety of physical–chemical parameters, including temperature, conductivity, light, oxygen and sulfide concentrations, and the community composition of anoxygenic phototrophic sulfur bacteria in the chemocline were recorded, to observe potential influence of external weather conditions. Our findings indicate that, despite the lake’s consistent physical and chemical stratification, the composition of the anoxygenic phototrophic sulfur bacteria community exhibited notable variations in response to external environmental factors, including changes in rainfall and light irradiance. Specifically, we observed different growth dynamics in the purple (PSB) and green (GSB) sulfur bacteria communities over the three years of monitoring. These variations underscore the complexity of biogeochemical cycles in meromictic lakes and the impact of external environmental factors on this ancestral microbial community dynamics. The results provide valuable insights into the stability of redox-stratified environments, offering a modern analog for ancient aquatic ecosystems. This research emphasizes the importance of long-term regular monitoring to capture interannual dynamics and assess the implications of climate change on such unique ecosystems.

Abstract Biological systems are currently analysed from deeper approaches considering not only their chemical features but also their quantum ones. Such elusive features sometimes account for specific phenomena related to their evolution and survival. Green sulphur bacteria are very simple microorganisms performing a highly photosynthetic process to survive. The Fenna-Mathew-Olson (FMO) complex is a macro-molecule responsible for such efficiency exhibiting interesting quantum features. Post-experimental biology together with Physics able the possibility to research and analyse them. In the current work, a synthetic roadmap for the FMO simulation is presented with comprehensive literature. The density matrix evolution is obtained to then discuss other derived features such as coherence, entanglement, state transference, and energy transmission efficiency.

In the process of anoxygenic photosynthesis phototrophic sulfur bacteria can use sulfides, thiosulfates, nitrites, bivalent iron, molecular hydrogen or organic compounds as exogenous electron donors and CO 2 as a carbon source. The influence of halides on transformed ecosystems, in particular, on their photosynthetic microbiota and its properties, remains insufficiently studied. The usage of nitrite and hydrogen sulfide ions as an electron donor of anoxygenic photosynthesis by cells of phototrophic purple and green sulfur bacteria Thiocapsa sp. Ya-2003, Lamprocystis sp. Ya-2003 and Chlorobium limicola IMV K-8, isolated from the Yavorivske Lake, under the influence of one of the most common toxicants, chlorine compounds, has been studied. Bacteria were cultivated under anaerobic conditions and constant lighting for 10 days in van Niel medium with NaNO 2 or Na 2 S×9H 2 O (4.2 mM). To study the influence of NaCl and C 6 H 4 ClNO 3 on biomass accumulation, nitrites or sulfides oxidation, nitrates or sulfates production, synthesis of intracellular carbohydrates, bacteria were sown in the media with chlorine compounds at co n centrations that are equal to the maximum permissible concentration (MPC) of chloride ions – 9.859 mM, and 0.5–4.0 (in NaCl composition) or 0.03–4.0 (in C 6 H 4 ClNO 3 composition) times differed from the MPC. Biomass was determined by the turbidim e tric method, the concentrations of nitrate, nitrite, hydrogen sulfide, sulfate ions in the cultural liquid – by the spectrophotometric method. The intracellular glucose and glycogen content was determined enzymatically in cell-free extracts of C. limicola IMV K-8, using the analytical kit “Diagluc-2”. It was found that NaCl at concentrations 3.0 – 4.0 times higher than the MPC significantly inhibits the biomass accumulation (2.2–2.8 times), NO₂⁻ oxidation (by 26.3–35.7%), and NO₃⁻ formation (1.6–1. 9 times) by all investigated strains of bacteria during growth in the medium with NaNO 2. Under the influence of NaCl at concentration 4.0 times exceeding the MPC the glycogen content in C. limicola IMV K-8 cells grown in the medium with NaNO 2 increased 2. 1 times compared to the control. NaCl at concentrations 2.0–4.0 times higher than the MPC significantly inhibits the biomass accumul a tion (2. 4 –2.6 times), HS⁻ oxidation ( by 42. 9–47. 5 %), and SO₄²⁻ formation (2. 9 –3. 1 times) by bacteria during growth in the m e dium with Na 2 S×9H 2 O. Under the influence of NaCl at concentration 4.0 times higher than the MPC the glycogen content in C. limicola IMV K-8 cells grown in the medium with Na 2 S×9H 2 O increased 2.2 times compared to the control. C 6 H 4 ClNO 3 at concentration 4.0 times higher than the MPC of chloride ions slightly inhibited the biomass accumulation (1. 3 –1.5 times), HS⁻ oxidation (by 15. 1 –22.2%), and SO₄²⁻ formation (1.5–1.6 times) by bacteria in the medium with Na 2 S×9H 2 O. Under the infl u ence of C 6 H 4 ClNO 3 at concentration 4.0 times higher than the MPC the glycogen content in C. limicola IMV K-8 cells grown in the medium with Na 2 S×9H 2 O increased 2 . 0 times compared to the control. Chloronitrophenol revealed a less toxic effect on changing the physiological properties of bacteria than sodium chloride at the same concentrations. Glycogen content in C. limic o la IMV K-8 cells grown in the medium with NaNO 2 and NaCl at concentration 4.0 times exceeding the MPC was the highest and amounted to 81. 7 mg/g dry cell weight. Since the ability of all tested strains of phototrophic bacteria to oxidize nitrites or hydr o gen sulfide remained sufficiently high even after adding chlorine compounds into the medium at concentrations 2.0–4.0 times exceeding the MPC of chloride ions, they are promising for use in technologies for cleaning environments with complex cont a mination by chlorine, sulfur, and nitrogen compounds.

Characterization of the intracellular polyphosphate granules of the phototrophic green sulfur bacterium Chlorobaculum tepidum

Anoxygenic phototrophic Fe(II) oxidizers (photoferrotrophs) are thought to have thrived in Earth’s ancient ferruginous oceans and played a primary role in the precipitation of Archaean and Palaeoproterozoic (3.8–1.85-billion-year-old) banded iron formations (BIFs). The end of BIF deposition by photoferrotrophs has been interpreted as the result of a deepening of water-column oxygenation below the photic zone, concomitant with the proliferation of cyanobacteria. However, photoferrotrophs may have experienced competition from other anaerobic Fe(II)-oxidizing microorganisms, altering the formation mechanism of BIFs. Here we utilize microbial incubations to show that nitrate-reducing Fe(II) oxidizers metabolically outcompete photoferrotrophs for dissolved Fe(II). Moreover, both experiments and numerical modelling show that the nitrate-reducing Fe(II) oxidizers inhibit photoferrotrophy via the production of toxic intermediates. Four different photoferrotrophs, representing both green sulfur and purple non-sulfur bacteria, are susceptible to this toxic effect despite having genomic capabilities for nitric oxide detoxification. Indeed, despite nitric oxide detoxification mechanisms being ubiquitous in some groups of phototrophs at the genomic level (for example, Chlorobi and Cyanobacteria) it is likely that they would still be affected. We suggest that the production of reactive nitrogen species during nitrate-reducing Fe(II) oxidation in ferruginous environments may have inhibited the activity of photoferrotrophs in the ancient oceans and thus impeded their role in the precipitation of BIFs.

Large-scale simulations of light-matter interaction in natural photosynthetic antenna complexes containing more than one hundred thousands of chlorophyll molecules, comparable with natural size, have been performed. Photosynthetic antenna complexes present in Green sulfur bacteria and Purple bacteria have been analyzed using a radiative non-Hermitian Hamiltonian, well-known in the field of quantum optics, instead of the widely used dipole-dipole Frenkel Hamiltonian. This approach allows us to study ensembles of emitters beyond the small volume limit (system size much smaller than the absorbed wavelength), where the Frenkel Hamiltonian fails. When analyzed on a large scale, such structures display superradiant states much brighter than their single components. An analysis of the robustness to static disorder and dynamical (thermal) noise shows that exciton coherence in the whole photosynthetic complex is larger than the coherence found in its parts. This provides evidence that the photosynthetic complex as a whole plays a predominant role in sustaining coherences in the system even at room temperature. Our results allow a better understanding of natural photosynthetic antennae and could drive experiments to verify how the response to electromagnetic radiation depends on the size of the photosynthetic antenna.

The relic Lake Mogilnoe, separated from the Barents Sea by a sand and pebble dam, is located in the high Arctic on the Kildin island (Murmansk region). This lake is a classic example of a meromictic basin of marine origin. The data obtained during the 2018 expedition showed changes in the hydrochemical regime of the lake that have occurred over the past 20 years. Sulfide concentration in the monimolimnion of the lake was as high as 140 mg/L. A tendency for salinization of the surface waters to 7 g/L has been noted. The Lake Mogilnoe is characterized by a discrepancy between the halocline and thermocline levels. The chemocline zone in the lake is below the halocline level. In a narrow oxygen-containing layer between 3 and 7.5 m, aerobic microflora of the marine type and marine fauna were present. The bacterial plate was formed at the boundary of the sulfide layer at ~8 m and mainly consisted of green sulfur bacteria (GSB). Brown-colored GSB species containing bacteriochlorophyll e were predominant. The previously formed concept of anaerobic phototrophic bacteria (APB) biodiversity based on morphological characteristics was modified using metagenomic data obtained by analyzing DNA from two samples of lake water in the chemocline zone, and was also supplemented by identifying new GSB species. Molecular diagnostic data confirmed the absolute dominance of the brackish species of GSB Chlorobium phaeovibrioides. This is the first on isolation and identification of brown- and green-colored Prosthecochloris aestuarii morphotypes from Lake Mogilnoe and identified, as well as of bacteriochlorophyll c-containing Prosthecochloris sp. The taxonomic position of Pelodyction phaem, which was constantly present in the Lake Mogilnoe, is discussed in detail. Despite the partial isolation of the ecosystem of Lake Mogilnoe from the Barents Sea, the main properties of the dominant GSB species of GSB and Prosthecochloris aestuarii turned out to be similar to those of the phylotypes living in lakes on the White Sea coast of the, which remained connected with the Barents Sea.

Anatomy of the late Famennian Dasberg event in a deep shelf of southern Euramerica: Oxygenation and productivity in a restricted basin during a progressive long-term cooling

Rapid sulfurization obscures carotenoid distributions in modern euxinic environments

Measurements of the spectral composition of light at the boundary of the photic zone in seven coastal bodies of water, to varying degrees separated from the sea, exposed to the sea and freshwater lake showed that in marine and brackish water bodies green light is predominantly transmitted, and in lakes the top layer of which is freshwater, orange, red and far red light is absorbed. In meromictic reservoirs, the photic zone was limited by a colored layer of water with the massive development of phototrophic microorganisms. Their pigment composition and the spectral composition of transmitted light are well matched. The sea bays and lagoons were dominated by taxa with red pigments: phycoerythrin-545 from cryptophyte algae, or purple sulfur bacteria with the carotenoid okenone, or brown-colored green sulfur bacteria with isorenieratin and bacteriochlorophyll e. In the lakes the top layer of which is freshwater, unicellular algae or green sulfur bacteria with chlorobactene and bacteriochlorophyll d developed. The spectral range can serve as a selective factor that determines the composition of the community of phototrophs with structurally different antennas, but similar light absorption spectra.

Reconstructing the palaeoecology of a middle Permian alkaline lake using molecular fossils, case study of the Lucaogou Formation in the Junggar Basin, NW China

The primary photochemical reaction of photosynthesis in green sulfur bacteria occurs in the homodimer PscA core proteins by a special chlorophyll pair. The light induced excited state of the special pair producing P840+ is rapidly reduced by electron transfer from one of the two PscC subunits. Molecular dynamics (MD) simulations are combined with bioinformatic tools herein to provide structural and dynamic insight into the complex between the two PscA core proteins and the two PscC subunits. The microscopic dynamic model involves extensive sampling at atomic resolution and at a cumulative time-scale of 22µs and reveals well defined protein–protein interactions. The membrane complex is composed of the two PscA and the two PscC subunits and macroscopic connections are revealed within a putative electron transfer pathway from the PscC subunit to the special pair P840 located within the PscA subunits. Our results provide a structural basis for understanding the electron transport to the homodimer RC of the green sulfur bacteria. The MD based approach can provide the basis to further probe the PscA-PscC complex dynamics and observe electron transfer therein at the quantum level. Furthermore, the transmembrane helices of the different PscC subunits exert distinct dynamics in the complex.

Observations of low-lying dark states in several photosynthetic complexes challenge our understanding of the mechanisms behind their efficient energy transfer processes. Computational models are necessary for providing novel insights into the nature and function of dark states, especially since these are not directly accessible in spectroscopy experiments. Here, we will focus on signatures of dark-type states in chlorosomes, a light-harvesting complex from green sulfur bacteria well-known for uniting a broad absorption band with very efficient energy transfer. In agreement with experiments, our simulations of two-dimensional electronic spectra capture the ultrafast exciton transfer occurring in 100s of femtoseconds within a single chlorosome cylinder. The sub-100 fs process corresponds to relaxation within the single-excitation manifold in a single chlorosome tube, where all initially created populations in the bright exciton states are quickly transferred to dark-type exciton states. Structural inhomogeneities on the local scale cause a redistribution of the oscillator strength, leading to the emergence of these dark-type exciton states, which dominate ultrafast energy transfer. The presence of the dark-type exciton states suppresses energy loss from an isolated chlorosome via fluorescence quenching, as observed experimentally. Our results further question whether relaxation to dark-exciton states is a leading process or merely competes with transfer to the baseplate within the photosynthetic apparatus of green sulfur bacteria.