Mechanisms of extracellular S0 globule production and degradation in Chlorobaculumtepidum via dynamic cell-globule interactions

Light and polyphosphate kinase 2 cooperatively regulate the production of zero-valent sulfur in a deep-sea bacterium

It is well established that different wavelengths of light exist in various deep-sea environments, and many deep-sea microorganisms have evolved specialized mechanisms for sensing and utilizing light energy. Our previous research found that blue light promotes zero-valent sulfur (ZVS) production in Erythrobacter flavus 21-3, a bacterium isolated from a deep-sea cold seep. Given that long-wavelength light is more prevalent in deep-sea environments, the present study investigates the mechanism by which E. flavus 21-3 senses infrared light (wavelength 940 nm) and regulates ZVS production. We found that the bacteriophytochrome BPHP-15570 is responsible for sensing infrared light, which induces autophosphorylation of BPHP-15570, activating the diguanylate cyclase DGC-0450 for c-di-GMP biosynthesis. Subsequently, the PilZ domain-containing protein mPilZ-1753 binds to c-di-GMP, triggering a well-established ZVS production pathway involving thiosulfate dehydrogenase (TsdA) and two homologs of thiosulfohydrolases (SoxB). Notably, polyphosphate kinase 2 (PPK2) is recruited to compete for GTP, the direct precursor of c-di-GMP biosynthesis. This competition downregulates ZVS production as well as other important metabolic processes. This negative regulatory pathway helps the bacterium avoid excessive ZVS accumulation, which could be toxic to bacterial growth. Overall, E. flavus 21-3 has evolved a sophisticated regulatory pathway to sense both blue and infrared light, triggering ZVS production. Our study provides a valuable model for understanding light utilization and its coupling with sulfur cycling in deep-sea environments.IMPORTANCEIt is widely believed that deep-sea ecosystems operate independently of light, relying primarily on chemical energy. However, the discovery of non-photosynthetic bacteria in various deep-sea environments that can sense and utilize light has challenged this assumption. In a recent study, we found that blue light significantly promotes the production of zero-valent sulfur (ZVS) in the deep-sea bacterium Erythrobacter flavus 21-3. Given that long-wavelength light is more prevalent in deep-sea environments, we investigated whether infrared light also plays a role in regulating ZVS production in E. flavus 21-3. Our results indicate that infrared light does promote ZVS formation in this bacterium. We identified PPK2 as a negative regulator, maintaining intracellular ZVS at safe levels to prevent toxicity due to excessive accumulation. Overall, our study offers a valuable model for exploring how light is utilized and its interaction with microbial sulfur cycling in the extreme conditions of the deep sea.

Pyrite stimulates the growth and sulfur oxidation capacity of anoxygenic phototrophic sulfur bacteria in euxinic environments

Anoxygenic phototrophic sulfur bacteria flourish in contemporary and ancient euxinic environments, driving the biogeochemical cycles of carbon and sulfur. However, it is unclear how these strict anaerobes meet their high demand for iron in iron-depleted environments. Here, we report that pyrite, a widespread and highly stable iron sulfide mineral in anoxic, low-temperature environments, can support the growth and metabolic activity of anoxygenic phototrophic sulfur bacteria by serving as the sole iron source under iron-depleted conditions. Transcriptomic and proteomic analyses revealed that pyrite addition substantially up-regulated genes and protein expression involved in photosynthesis, sulfur metabolism, and biosynthesis of organics. Anoxic microbial oxidation of pyritic sulfur and consequent destabilization of the pyrite structure were postulated to facilitate microbial iron acquisition. These findings advance our understanding of the survival strategies of anaerobes in iron-depleted environments and are important for revealing the previously underappreciated bioavailability of pyritic iron in anoxic environments and anoxic weathering of pyrite.

Anoxygenic photosynthesis with emphasis on green sulfur bacteria and a perspective for hydrogen sulfide detoxification of anoxic environments

The bacterial light-dependent energy metabolism can be divided into two types: oxygenic and anoxygenic photosynthesis. Bacterial oxygenic photosynthesis is similar to plants and is characteristic for cyanobacteria. Bacterial anoxygenic photosynthesis is performed by anoxygenic phototrophs, especially green sulfur bacteria (GSB; family Chlorobiaceae) and purple sulfur bacteria (PSB; family Chromatiaceae). In anoxygenic photosynthesis, hydrogen sulfide (H2S) is used as the main electron donor, which differs from plants or cyanobacteria where water is the main source of electrons. This review mainly focuses on the microbiology of GSB, which may be found in water or soil ecosystems where H2S is abundant. GSB oxidize H2S to elemental sulfur. GSB possess special structures-chlorosomes-wherein photosynthetic pigments are located. Chlorosomes are vesicles that are surrounded by a lipid monolayer that serve as light-collecting antennas. The carbon source of GSB is carbon dioxide, which is assimilated through the reverse tricarboxylic acid cycle. Our review provides a thorough introduction to the comparative eco-physiology of GSB and discusses selected application possibilities of anoxygenic phototrophs in the fields of environmental management, bioremediation, and biotechnology.

Quantitative proteomics reveals the Sox system's role in sulphur and arsenic metabolism of phototroph Halorhodospira halophila

The metabolic process of purple sulphur bacteria's anoxygenic photosynthesis has been primarily studied in Allochromatium vinosum, a member of the Chromatiaceae family. However, the metabolic processes of purple sulphur bacteria from the Ectothiorhodospiraceae and Halorhodospiraceae families remain unexplored. We have analysed the proteome of Halorhodospira halophila, a member of the Halorhodospiraceae family, which was cultivated with various sulphur compounds. This analysis allowed us to reconstruct the first comprehensive sulphur-oxidative photosynthetic network for this family. Some members of the Ectothiorhodospiraceae family have been shown to use arsenite as a photosynthetic electron donor. Therefore, we analysed the proteome response of Halorhodospira halophila when grown under arsenite and sulphide conditions. Our analyses using ion chromatography-inductively coupled plasma mass spectrometry showed that thioarsenates are chemically formed under these conditions. However, they are more extensively generated and converted in the presence of bacteria, suggesting a biological process. Our quantitative proteomics revealed that the SoxAXYZB system, typically dedicated to thiosulphate oxidation, is overproduced under these growth conditions. Additionally, two electron carriers, cytochrome c551/c5 and HiPIP III, are also overproduced. Electron paramagnetic resonance spectroscopy suggested that these transporters participate in the reduction of the photosynthetic Reaction Centre. These results support the idea of a chemically and biologically formed thioarsenate being oxidized by the Sox system, with cytochrome c551/c5 and HiPIP III directing electrons towards the Reaction Centre.

Microorganisms uptake zero-valent sulfur via membrane lipid dissolution of octasulfur and intracellular solubilization as persulfide

Zero-valent sulfur, commonly utilized as a fertilizer or fungicide, is prevalent in various environmental contexts. Its most stable and predominant form, octasulfur (S8), plays a crucial role in microbial sulfur metabolism, either through oxidation or reduction. However, the mechanism underlying its cellular uptake remains elusive. We presented evidence that zero-valent sulfur was adsorbed to the cell surface and then dissolved into the membrane lipid layer as lipid-soluble S8 molecules, which reacted with cellular low-molecular thiols to form persulfide, e.g., glutathione persulfide (GSSH), in the cytoplasm. The process brought extracellular zero-valent sulfur into the cells. When persulfide dioxygenase is present in the cells, GSSH will be oxidized. Otherwise, GSSH will react with another glutathione (GSH) to produce glutathione disulfide (GSSG) and hydrogen sulfide (H2S). The mechanism is different from simple diffusion, as insoluble S8 becomes soluble GSSH after crossing the cytoplasmic membrane. The uptake process is limited by physical contact of insoluble zero-valent sulfur with microbial cells and the regeneration of cellular thiols. Our findings elucidate the cellular uptake mechanism of zero-valent sulfur, which provides critical information for its application in agricultural practices and the bioremediation of sulfur contaminants and heavy metals.

Fluorescence Microscopy Study of the Intracellular Sulfur Globule Protein SgpD in the Purple Sulfur Bacterium Allochromatium vinosum

When oxidizing reduced sulfur compounds, the phototrophic sulfur bacterium Allochromatium vinosum forms spectacular sulfur globules as obligatory intracellular-but extracytoplasmic-intermediates. The globule envelope consists of three extremely hydrophobic proteins: SgpA and SgpB, which are very similar and can functionally replace each other, and SgpC which is involved in the expansion of the sulfur globules. The presence of a fourth protein, SgpD, was suggested by comparative transcriptomics and proteomics of purified sulfur globules. Here, we investigated the in vivo function of SgpD by coupling its carboxy-terminus to mCherry. This fluorescent protein requires oxygen for chromophore maturation, but we were able to use it in anaerobically growing A. vinosum provided the cells were exposed to oxygen for one hour prior to imaging. While mCherry lacking a signal peptide resulted in low fluorescence evenly distributed throughout the cell, fusion with SgpD carrying its original Sec-dependent signal peptide targeted mCherry to the periplasm and co-localized it exactly with the highly light-refractive sulfur deposits seen in sulfide-fed A. vinosum cells. Insertional inactivation of the sgpD gene showed that the protein is not essential for the formation and degradation of sulfur globules.

Blue light promotes zero-valent sulfur production in a deep-sea bacterium

Increasing evidence has shown that light exists in a diverse range of deep-sea environments. We unexpectedly found that blue light is necessary to produce excess zero-valent sulfur (ZVS) in Erythrobacter flavus 21-3, a bacterium that has been recently isolated from a deep-sea cold seep. E. flavus 21-3 is able to convert thiosulfate to ZVS using a novel thiosulfate oxidation pathway comprising a thiosulfate dehydrogenase (TsdA) and a thiosulfohydrolase (SoxB). Using proteomic, bacterial two-hybrid and heterologous expression assays, we found that the light-oxygen-voltage histidine kinase LOV-1477 responds to blue light and activates the diguanylate cyclase DGC-2902 to produce c-di-GMP. Subsequently, the PilZ domain-containing protein mPilZ-1753 binds to c-di-GMP and activates TsdA through direct interaction. Finally, Raman spectroscopy and gene knockout results verified that TsdA and two SoxB homologs cooperate to regulate ZVS production. As ZVS is an energy source for E. flavus 21-3, we propose that deep-sea blue light provides E. flavus 21-3 with a selective advantage in the cold seep, suggesting a previously unappreciated relationship between light-sensing pathways and sulfur metabolism in a deep-sea microorganism.

Insights into the sulfur metabolism of Chlorobaculum tepidum by label-free quantitative proteomics

Chlorobaculum tepidum is an anaerobic green sulfur bacterium which oxidizes sulfide, elemental sulfur, and thiosulfate for photosynthetic growth. It can also oxidize sulfide to produce extracellular S0 globules, which can be further oxidized to sulfate and used as an electron donor. Here, we performed label-free quantitative proteomics on total cell lysates prepared from different metabolic states, including a sulfur production state (10 h post-incubation [PI]), the beginning of sulfur consumption (20 h PI), and the end of sulfur consumption (40 h PI), respectively. We observed an increased abundance of the sulfide:quinone oxidoreductase (Sqr) proteins in 10 h PI indicating a sulfur production state. The periplasmic thiosulfate-oxidizing Sox enzymes and the dissimilatory sulfite reductase (Dsr) subunits showed an increased abundance in 20 h PI, corresponding to the sulfur-consuming state. In addition, we found that the abundance of the heterodisulfide-reductase and the sulfhydrogenase operons was influenced by electron donor availability and may be associated with sulfur metabolism. Further, we isolated and analyzed the extracellular sulfur globules in the different metabolic states to study their morphology and the sulfur cluster composition, yielding 58 previously uncharacterized proteins in purified globules. Our results show that C. tepidum regulates the cellular levels of enzymes involved in sulfur metabolism in response to the availability of reduced sulfur compounds.

Removal of small elemental sulfur particles by polysulfide formation in a sulfidic reactor

For over 30 years, biological gas desulfurization under halo-alkaline conditions has been studied and optimized. This technology is currently applied in already 270 commercial installations worldwide. Sulfur particle separation, however, remains a challenge; a fraction of sulfur particles is often too small for liquid-solid separation with conventional separation technology. In this article, we report the effects of a novel sulfidic reactor, inserted in the conventional process set-up, on sulfur particle size and morphology. In the sulfidic reactor polysulfide is produced by the reaction of elemental sulfur particles and sulfide, which is again converted to elemental sulfur in a gas-lift reactor. We analyzed sulfur particles produced in continuous, long term lab-scale reactor experiments under various sulfide concentrations and sulfidic retention times. The analyses were performed with laser diffraction particle size analysis and light microscopy. These show that the smallest particles (< 1 µm) have mostly disappeared under the highest sulfide concentration (4.1 mM) and sulfidic retention time (45 min). Under these conditions also agglomeration of sulfur particles was promoted. Model calculations with thermodynamic and previously derived kinetic data on polysulfide formation confirm the experimental data on the removal of the smallest particles. Under the 'highest sulfidic pressure', the model predicts that equilibrium conditions are reached between sulfur, sulfide and polysulfide and that 100% of the sulfur particles <1 µm are dissolved by the (autocatalytic) formation of polysulfides. These experiments and modeling results demonstrate that the insertion of a novel sulfidic reactor in the conventional process set-up promotes the removal of the smallest individual sulfur particles and promotes the production of sulfur agglomerates. The novel sulfidic reactor is therefore a promising process addition with the potential to improve process operation, sulfur separation and sulfur recovery.

Sulfide removal characteristics, pathways and potential application of a novel chemolithotrophic sulfide-oxidizing strain, Marinobacter sp. SDSWS8

Sulfide generally exists in wastewater, black and odor river, as well as aquaculture water, and give rise to adverse effect on ecological stability and biological safety, due to the toxicity, corrosivity and malodor of sulfide. In the present study, a chemolithotrophic sulfide-oxidizing bacteria (SOB) was isolated and identified as Marinobacter maroccanus strain SDSWS8. And it produced no hemolysin and was susceptible to most antibiotics. There were no accumulation of sulfide, sulfate and thiosulfate during the sulfide removal process. The optimum conditions of sulfide removal were temperature 15-40 °C, initial pH value 4.5-9.5, salinity 10-40‰, C/N ratio 0-20 and sulfide concentration 25-150 mg/L. The key genes of sulfide oxidation, Sox system (soxB, soxX, soxA, soxZ, soxY, soxD, soxC), dissimilatory sulfur oxidation (dsrA, aprA and sat) and sqr, were successfully amplified and expressed, indicating the three pathways coordinated to complete the sulfide oxidation. Besides, strain SDSWS8 had inhibitory effect on four pathogen Vibrio (V. harveyi, V. parahaemolyticus, V. anguillarum and V. splendidus). Furthermore, efficient removal of sulfide from real aquaculture water and sludge mixture could be accomplished by strain SDSWS8. This study may provide a promising candidate strain for sulfide-rich water treatment.

Organic layer characteristics and microbial utilization of the biosulfur globules produced by haloalkaliphilic Thioalkalivibrio versutus D301 during biological desulfurization

The haloalkaliphilic genus Thioalkalivibrio, widely used in bio-desulfurization, can oxidize H₂S to S^o, which is excreted outside cells in the form of biosulfur globules. As by-product of bio-desulfurization, information on biosulfur globules is still very scant, which limits its high-value utilization. In this paper, the characteristics of biosulfur globules produced by Thioalkalivibrio versutus D301 and the possibility of cultivating sulfur-oxidizing bacteria as a high biological-activity sulfur source were studied. The sulfur element in the biosulfur globules existed in the form α-S₈, which was similar to chemical sulfur. The biosulfur globule was wrapped with an organic layer composed of polysaccharides and proteins. The composition of this organic layer could change. In the formation stage of biosulfur globules, the organic layer was dominated by polysaccharides, and in later stage, proteins became the main component. We speculated that the organic layer was mainly formed by the passive adsorption of organic matter secreted by cells. The existence of organic layer endowed biosulfur with better bioavailability. Compared with those found using chemical sulfur, the growth rates of Acidithiobacillus thiooxidans ATCC 19377^T, Thiomicrospira microaerophila BDL05 and Thioalkalibacter halophilus BDH06 using biosulfur increased several folds to an order of magnitude, indicating that biosulfur was a good sulfur source for cultivating sulfur-oxidizing bacteria.

Into the darkness: the ecologies of novel 'microbial dark matter' phyla in an Antarctic lake

Uncultivated microbial clades ('microbial dark matter') are inferred to play important but uncharacterized roles in nutrient cycling. Using Antarctic lake (Ace Lake, Vestfold Hills) metagenomes, 12 metagenome-assembled genomes (MAGs; 88%-100% complete) were generated for four 'dark matter' phyla: six MAGs from Candidatus Auribacterota (=Aureabacteria, SURF-CP-2), inferred to be hydrogen- and sulfide-producing fermentative heterotrophs, with individual MAGs encoding bacterial microcompartments (BMCs), gas vesicles, and type IV pili; one MAG (100% complete) from Candidatus Hinthialibacterota (=OLB16), inferred to be a facultative anaerobe capable of dissimilatory nitrate reduction to ammonia, specialized for mineralization of complex organic matter (e.g. sulfated polysaccharides), and encoding BMCs, flagella, and Tad pili; three MAGs from Candidatus Electryoneota (=AABM5-125-24), previously reported to include facultative anaerobes capable of dissimilatory sulfate reduction, and here inferred to perform sulfite oxidation, reverse tricarboxylic acid cycle for autotrophy, and possess numerous proteolytic enzymes; two MAGs from Candidatus Lernaellota (=FEN-1099), inferred to be capable of formate oxidation, amino acid fermentation, and possess numerous enzymes for protein and polysaccharide degradation. The presence of 16S rRNA gene sequences in public metagenome datasets (88%-100% identity) suggests these 'dark matter' phyla contribute to sulfur cycling, degradation of complex organic matter, ammonification and/or chemolithoautotrophic CO2 fixation in diverse global environments.

Small RNAs beyond Model Organisms: Have We Only Scratched the Surface?

Small RNAs (sRNAs) are essential regulators in the adaptation of bacteria to environmental changes and act by binding targeted mRNAs through base complementarity. Approximately 550 distinct families of sRNAs have been identified since their initial characterization in the 1980s, accelerated by the emergence of RNA-sequencing. Small RNAs are found in a wide range of bacterial phyla, but they are more prominent in highly researched model organisms compared to the rest of the sequenced bacteria. Indeed, Escherichia coli and Salmonella enterica contain the highest number of sRNAs, with 98 and 118, respectively, with Enterobacteriaceae encoding 145 distinct sRNAs, while other bacteria families have only seven sRNAs on average. Although the past years brought major advances in research on sRNAs, we have perhaps only scratched the surface, even more so considering RNA annotations trail behind gene annotations. A distinctive trend can be observed for genes, whereby their number increases with genome size, but this is not observable for RNAs, although they would be expected to follow the same trend. In this perspective, we aimed at establishing a more accurate representation of the occurrence of sRNAs in bacteria, emphasizing the potential for novel sRNA discoveries.

Shedding Light on Microbial "Dark Matter": Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake

The potential metabolism and ecological roles of many microbial taxa remain unknown because insufficient genomic data are available to assess their functional potential. Two such microbial "dark matter" taxa are the Candidatus bacterial phyla Cloacimonadota and Omnitrophota, both of which have been identified in global anoxic environments, including (but not limited to) organic-carbon-rich lakes. Using 24 metagenome-assembled genomes (MAGs) obtained from an Antarctic lake (Ace Lake, Vestfold Hills), novel lineages and novel metabolic traits were identified for both phyla. The Cloacimonadota MAGs exhibited a capacity for carbon fixation using the reverse tricarboxylic acid cycle driven by oxidation of hydrogen and sulfur. Certain Cloacimonadota MAGs encoded proteins that possess dockerin and cohesin domains, which is consistent with the assembly of extracellular cellulosome-like structures that are used for degradation of polypeptides and polysaccharides. The Omnitrophota MAGs represented phylogenetically diverse taxa that were predicted to possess a strong biosynthetic capacity for amino acids, nucleosides, fatty acids, and essential cofactors. All of the Omnitrophota were inferred to be obligate fermentative heterotrophs that utilize a relatively narrow range of organic compounds, have an incomplete tricarboxylic acid cycle, and possess a single hydrogenase gene important for achieving redox balance in the cell. We reason that both Cloacimonadota and Omnitrophota form metabolic interactions with hydrogen-consuming partners (methanogens and Desulfobacterota, respectively) and, therefore, occupy specific niches in Ace Lake.

Novel Agglomeration Strategy for Elemental Sulfur Produced during Biological Gas Desulfurization

This article presents a novel crystal agglomeration strategy for elemental sulfur (S) produced during biological desulfurization (BD). A key element is the nucleophilic dissolution of S by sulfide (HS-) to polysulfides (S x 2-), which was enhanced by a sulfide-rich, anoxic reactor. This study demonstrates that with enhanced S x 2- formation, crystal agglomerates are formed with a uniform size (14.7 ± 3.1 μm). In contrast, with minimal S x 2- formation, particle size fluctuates markedly (5.6 ± 5.9 μm) due to the presence of agglomerates and single crystals. Microscopic analysis showed that the uniformly sized agglomerates had an irregular structure, whereas the loose particles and agglomerates were more defined and bipyramidal. The irregular agglomerates are explained by dissolution of S by (poly)sulfides, which likely changed the crystal surface structure and disrupted crystal growth. Furthermore, S from S x 2- appeared to form at least 5× faster than from HS- based on the average S x 2- chain length of x ≈ 5, thereby stimulating particle agglomeration. In addition, microscopy suggested that S crystal growth proceeded via amorphous S globules. Our findings imply that the crystallization product is controlled by the balance between dissolution and formation of S. This new insight has a strong potential to prevent poor S settleability in BD.

Organic Stabilization of Extracellular Elemental Sulfur in a Sulfurovum-Rich Biofilm: A New Role for Extracellular Polymeric Substances?

This work shines light on the role of extracellular polymeric substance (EPS) in the formation and preservation of elemental sulfur biominerals produced by sulfur-oxidizing bacteria. We characterized elemental sulfur particles produced within a Sulfurovum-rich biofilm in the Frasassi Cave System (Italy). The particles adopt spherical and bipyramidal morphologies, and display both stable (α-S8) and metastable (β-S8) crystal structures. Elemental sulfur is embedded within a dense matrix of EPS, and the particles are surrounded by organic envelopes rich in amide and carboxylic groups. Organic encapsulation and the presence of metastable crystal structures are consistent with elemental sulfur organomineralization, i.e., the formation and stabilization of elemental sulfur in the presence of organics, a mechanism that has previously been observed in laboratory studies. This research provides new evidence for the important role of microbial EPS in mineral formation in the environment. We hypothesize that the extracellular organics are used by sulfur-oxidizing bacteria for the stabilization of elemental sulfur minerals outside of the cell wall as a store of chemical energy. The stabilization of energy sources (in the form of a solid electron acceptor) in biofilms is a potential new role for microbial EPS that requires further investigation.

Vertical structure of the bacterial diversity in meromictic Fayetteville Green Lake

The permanently stratified water columns in euxinic meromictic lakes produce niche environments for phototrophic sulfur oxidizers and diverse sulfur metabolisms. While Green Lake (Fayetteville, New York, NY) is known to host a diverse community of ecologically important sulfur bacteria, analyses of its microbial communities, to date, have been largely based on pigment analysis and smaller datasets from Sanger sequencing techniques. Here, we present the results of next-generation sequencing of the eubacterial community in the context of the water column geochemistry. We observed abundant purple and green sulfur bacteria, as well as anoxygenic photosynthesis-capable cyanobacteria within the upper monimolimnion. Amidst the phototrophs, we found other sulfur-cycling bacteria including sulfur disproportionators and chemotrophic sulfur oxidizers, further detailing our understanding of the sulfur cycle and microbial ecology of euxinic, meromictic lakes.

Microbially-driven sulfur cycling microbial communities in different mangrove sediments

Microbially-driven sulfur cycling is a vital biogeochemical process in the sulfur-rich mangrove ecosystem. It is critical to evaluate the potential impact of sulfur transformation in mangrove ecosystems. To reveal the diversity, composition, and structure of sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) and underlying mechanisms, we analyzed the physicochemical properties and sediment microbial communities from an introduced mangrove species (Sonneratia apetala), a native mangrove species (Kandelia obovata) and the mudflat in Hanjiang River Estuary in Guangdong (23.27°N, 116.52°E), China. The results indicated that SOB was dominated by autotrophic Thiohalophilus and chemoautotrophy Chromatium in S. apetala and K. obovata, respectively, while Desulfatibacillum was the dominant genus of SRB in K. obovata sediments. Also, the redundancy analysis indicated that temperature, redox potential (ORP), and SO₄^2- were the significant factors influencing the sulfur cycling microbial communities with elemental sulfur (ES) as the key factor driver for SOB and total carbon (TC) for SRB in mangrove sediments. Additionally, the morphological transformation of ES, acid volatile sulfide (AVS) and SO₄^2- explained the variation of sulfur cycling microbial communities under sulfur-rich conditions, and we found mangrove species-specific dominant Thiohalobacter, Chromatium and Desulfatibacillum, which could well use ES and SO₄^2-, thus promoting the sulfur cycling in mangrove sediments. Meanwhile, the change of nutrient substances (TN, TC) explained why SOB were more susceptible to environmental changes than SRB. Sulfate reducing bacteria produces sulfide in anoxic sediments at depth that then migrate upward, toward fewer reducing conditions, where it's oxidized by sulfur oxidizing bacteria. This study indicates the high ability of SOB and SRB in ES, SO₄^2-_,S₂^- and S^2- generation and transformation in sulfur-rich mangrove ecosystems, and provides novel insights into sulfur cycling in other wetland ecosystems from a microbial perspective.

Characterization of Sulfurimonas hydrogeniphila sp. nov., a Novel Bacterium Predominant in Deep-Sea Hydrothermal Vents and Comparative Genomic Analyses of the Genus Sulfurimonas

Bacteria of the genus Sulfurimonas within the class Campylobacteria are predominant in global deep-sea hydrothermal environments and widespread in global oceans. However, only few bacteria of this group have been isolated, and their adaptations for these extreme environments remain poorly understood. Here, we report a novel mesophilic, hydrogen- and sulfur-oxidizing bacterium, strain NW10T, isolated from a deep-sea sulfide chimney of Northwest Indian Ocean.16S rRNA gene sequence analysis showed that strain NW10T was most closely related to the vent species Sulfurimonas paralvinellae GO25T with 95.8% similarity, but ANI and DDH values between two strains were only 19.20 and 24.70%, respectively, indicating that strain NW10 represents a novel species. Phenotypic characterization showed strain NW10T is an obligate chemolithoautotroph utilizing thiosulfate, sulfide, elemental sulfur, or molecular hydrogen as energy sources, and molecular oxygen, nitrate, or elemental sulfur as electron acceptors. Moreover, hydrogen supported a better growth than reduced sulfur compounds. During thiosulfate oxidation, the strain can produce extracellular sulfur of elemental α-S8 with an unknown mechanism. Polyphasic taxonomy results support that strain NW10T represents a novel species of the genus Sulfurimonas, and named as Sulfurimonas hydrogeniphila sp. nov. Genome analyses revealed its diverse energy metabolisms driving carbon fixation via rTCA cycling, including pathways of sulfur/hydrogen oxidation, coupled oxygen/sulfur respiration and denitrification. Comparative analysis of the 11 available genomes from Sulfurimonas species revealed that vent bacteria, compared to marine non-vent strains, possess unique genes encoding Type V Sqr, Group II, and Coo hydrogenase, and are selectively enriched in genes related to signal transduction and inorganic ion transporters. These phenotypic and genotypic features of vent Sulfurimonas may explain their thriving in hydrothermal environments and help to understand the ecological role of Sulfurimonas bacteria in hydrothermal ecosystems.

Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community

BACKGROUND

Cold environments dominate the Earth's biosphere and microbial activity drives ecosystem processes thereby contributing greatly to global biogeochemical cycles. Polar environments differ to all other cold environments by experiencing 24-h sunlight in summer and no sunlight in winter. The Vestfold Hills in East Antarctica contains hundreds of lakes that have evolved from a marine origin only 3000-7000 years ago. Ace Lake is a meromictic (stratified) lake from this region that has been intensively studied since the 1970s. Here, a total of 120 metagenomes representing a seasonal cycle and four summers spanning a 10-year period were analyzed to determine the effects of the polar light cycle on microbial-driven nutrient cycles.

RESULTS

The lake system is characterized by complex sulfur and hydrogen cycling, especially in the anoxic layers, with multiple mechanisms for the breakdown of biopolymers present throughout the water column. The two most abundant taxa are phototrophs (green sulfur bacteria and cyanobacteria) that are highly influenced by the seasonal availability of sunlight. The extent of the Chlorobium biomass thriving at the interface in summer was captured in underwater video footage. The Chlorobium abundance dropped from up to 83% in summer to 6% in winter and 1% in spring, before rebounding to high levels. Predicted Chlorobium viruses and cyanophage were also abundant, but their levels did not negatively correlate with their hosts.

CONCLUSION

Over-wintering expeditions in Antarctica are logistically challenging, meaning insight into winter processes has been inferred from limited data. Here, we found that in contrast to chemolithoautotrophic carbon fixation potential of Southern Ocean Thaumarchaeota, this marine-derived lake evolved a reliance on photosynthesis. While viruses associated with phototrophs also have high seasonal abundance, the negative impact of viral infection on host growth appeared to be limited. The microbial community as a whole appears to have developed a capacity to generate biomass and remineralize nutrients, sufficient to sustain itself between two rounds of sunlight-driven summer-activity. In addition, this unique metagenome dataset provides considerable opportunity for future interrogation of eukaryotes and their viruses, abundant uncharacterized taxa (i.e. dark matter), and for testing hypotheses about endemic species in polar aquatic ecosystems. Video Abstract.

Epiphytic bacterial community shift drives the nutrient cycle during Potamogeton malaianus decomposition

Epiphytic bacteria on submerged macrophytes play important roles in the nutrient cycle in freshwater ecosystems. However, little is known about the composition and role of epiphytic bacteria during the decomposition of submerged macrophytes. In this study, the alterations in epiphytic bacterial composition, abundances of nitrogen cycle-related genes and nutrient release were investigated in a 56-day decomposition process of Potamogeton malaianus. The total reduced biomass was positively related to the contents of carbon, nitrogen and phosphorus released from plant residues. Nutrient released from plant litter showed a positively effect on the concentrations of carbon, nitrogen and phosphorus in the overlying water (p < 0.01). The carbon, phosphorus and nitrogen decreased with decomposition process in both plant debris and overlying water. Humic acid-like substances were the main component of dissolved organic matter in the conditioning stage, whereas fulvic acid-like substances dominated in the fragmentation stage. Results from network analysis and canonical correspondence analysis showed dominant bacterial clades changed with decomposition process. Bacteroidetes was the most abundant phylum in the leaching stage and Spirochaetes, Chlorobi, and Bacteroidetes dominated in the conditioning stage, while Chlorobi dominated in the fragmentation stage. The highest abundance of cnorB and nosZ were detected in the leaching and fragmentation stage, respectively. Bacterial denitrification contributed to nitrogen removal and might be promoted by high ORP and DOC concentration. Our results indicate that epiphytic bacterial community shift drived the metabolism of nutrients C, N, and S during the decomposition of P. malaianus.

Elemental Sulfur Formation by Sulfuricurvum kujiense Is Mediated by Extracellular Organic Compounds

Elemental sulfur [S(0)] is a central and ecologically important intermediate in the sulfur cycle, which can be used by a wide diversity of microorganisms that gain energy from its oxidation, reduction, or disproportionation. S(0) is formed by oxidation of reduced sulfur species, which can be chemically or microbially mediated. A variety of sulfur-oxidizing bacteria can biomineralize S(0), either intracellularly or extracellularly. The details and mechanisms of extracellular S(0) formation by bacteria have been in particular understudied so far. An important question in this respect is how extracellular S(0) minerals can be formed and remain stable in the environment outside of their thermodynamic stability domain. It was recently discovered that S(0) minerals could be formed and stabilized by oxidizing sulfide in the presence of dissolved organic compounds, a process called S(0) organomineralization. S(0) particles formed through this mechanism possess specific signatures such as morphologies that differ from that of their inorganically precipitated counterparts, encapsulation within an organic envelope, and metastable crystal structures (presence of the monoclinic β- and γ-S₈ allotropes). Here, we investigated S(0) formation by the chemolithoautotrophic sulfur-oxidizing and nitrate-reducing bacterium Sulfuricurvum kujiense (Epsilonproteobacteria). We performed a thorough characterization of the S(0) minerals produced extracellularly in cultures of this microorganism, and showed that they present all the specific signatures (morphology, association with organics, and crystal structures) of organomineralized S(0). Using "spent medium" experiments, we furthermore demonstrated that soluble extracellular compounds produced by S. kujiense are necessary to form and stabilize S(0) minerals outside of the cells. This study provides the first experimental evidence of the importance of organomineralization in microbial S(0) formation. The prevalence of organomineralization in extracellular S(0) precipitation by other sulfur bacteria remains to be investigated, and the biological role of this mechanism is still unclear. However, we propose that sulfur-oxidizing bacteria could use soluble organics to stabilize stores of bioavailable S(0) outside the cells.

Low frequency Raman Spectroscopy for micron-scale and in vivo characterization of elemental sulfur in microbial samples

Elemental sulfur (S(0)) is an important intermediate of the sulfur cycle and is generated by chemical and biological sulfide oxidation. Raman spectromicroscopy can be applied to environmental samples for the detection of S(0), as a practical non-destructive micron-scale method for use on wet material and living cells. Technical advances in filter materials enable the acquisition of ultra-low frequency (ULF) Raman measurements in the 10–100 cm⁻¹ range using a single-stage spectrometer. Here we demonstrate the potency of ULF Raman spectromicroscopy to harness the external vibrational modes of previously unrecognized S(0) structures present in environmental samples. We investigate the chemical and structural nature of intracellular S(0) granules stored within environmental mats of sulfur-oxidizing γ-Proteobacteria (Thiothrix). In vivo intracellular ULF scans indicate the presence of amorphous cyclooctasulfur (S₈), clarifying enduring uncertainties regarding the content of microbial sulfur storage globules. Raman scattering of extracellular sulfur clusters in Thiothrix mats furthermore reveals an unexpected abundance of metastable β-S₈ and γ-S₈, in addition to the stable α-S₈ allotrope. We propose ULF Raman spectroscopy as a powerful method for the micron-scale determination of S(0) structure in natural and laboratory systems, with a promising potential to shine new light on environmental microbial and chemical sulfur cycling mechanisms.

Insight Into Interactions of Thermoacidophilic Archaea With Elemental Sulfur: Biofilm Dynamics and EPS Analysis

Biooxidation of reduced inorganic sulfur compounds (RISCs) by thermoacidophiles is of particular interest for the biomining industry and for environmental issues, e.g., formation of acid mine drainage (AMD). Up to now, interfacial interactions of acidophiles with elemental sulfur as well as the mechanisms of sulfur oxidation by acidophiles, especially thermoacidophiles, are not yet fully clear. This work focused on how a crenarchaeal isolate Acidianus sp. DSM 29099 interacts with elemental sulfur. Analysis by Confocal laser scanning microscopy (CLSM) and Atomic force microscopy (AFM) in combination with Epifluorescence microscopy (EFM) shows that biofilms on elemental sulfur are characterized by single colonies and a monolayer in first stage and later on 3-D structures with a diameter of up to 100 μm. The analysis of extracellular polymeric substances (EPS) by a non-destructive lectin approach (fluorescence lectin-barcoding analysis) using several fluorochromes shows that intial attachment was featured by footprints rich in biofilm cells that were embedded in an EPS matrix consisting of various glycoconjugates. Wet chemistry data indicate that carbohydrates, proteins, lipids and uronic acids are the main components. Attenuated reflectance (ATR)-Fourier transformation infrared spectroscopy (FTIR) and high-performance anion exchange chromatography with pulsed amperometric detection (HPAE-PAD) indicate glucose and mannose as the main monosaccharides in EPS polysaccharides. EPS composition as well as sugar types in EPS vary according to substrate (sulfur or tetrathionate) and lifestyle (biofilms and planktonic cells). This study provides information on the building blocks/make up as well as dynamics of biofilms of thermoacidophilic archaea in extremely acidic environments.

Insights Into the Mineralogy and Surface Chemistry of Extracellular Biogenic S0 Globules Produced by Chlorobaculum tepidum

Elemental sulfur (S0) is produced and degraded by phylogenetically diverse groups of microorganisms. For Chlorobaculum tepidum, an anoxygenic phototroph, sulfide is oxidized to produce extracellular S0 globules, which can be further oxidized to sulfate. While some sulfur-oxidizing bacteria (e.g., Allochromatium vinosum) are also capable of growth on commercial S0 as an electron donor, C. tepidum is not. Even colloidal sulfur sols, which appear indistinguishable from biogenic globules, do not support the growth of C. tepidum. Here, we investigate the properties that make biogenic S0 globules distinct from abiotic forms of S0. We found that S0 globules produced by C. tepidum and abiotic S0 sols are quite similar in terms of mineralogy and material properties, but the two are distinguished primarily by the properties of their surfaces. C. tepidum's globules are enveloped by a layer of organics (protein and polysaccharides), which results in a surface that is fundamentally different from that of abiotic S0 sols. The organic coating on the globules appears to slow the aging and crystallization of amorphous sulfur, perhaps providing an extended window of time for microbes in the environment to access the more labile forms of sulfur as needed. Overall, our results suggest that the surface of biogenic S0 globules may be key to cell-sulfur interactions and the reactivity of biogenic S0 in the environment.

The role of polysulfide dianions and radical anions in the chemical, physical and biological sciences, including sulfur-based batteries

Polysulfide dianions and radical anions play a crucial role in biological chemistry, geochemical processes, alkali metal–sulfur batteries, organic syntheses, coordination chemistry, and materials sciences.

Differential RNA Sequencing Implicates Sulfide as the Master Regulator of S0 Metabolism in Chlorobaculum tepidum and Other Green Sulfur Bacteria

The green sulfur bacteria (Chlorobiaceae) are anaerobes that use electrons from reduced sulfur compounds (sulfide, S⁰, and thiosulfate) as electron donors for photoautotrophic growth. Chlorobaculum tepidum, the model system for the Chlorobiaceae, both produces and consumes extracellular S⁰ globules depending on the availability of sulfide in the environment. These physiological changes imply significant changes in gene regulation, which has been observed when sulfide is added to Cba. tepidum growing on thiosulfate. However, the underlying mechanisms driving these gene expression changes, i.e., the specific regulators and promoter elements involved, have not yet been defined. Here, differential RNA sequencing (dRNA-seq) was used to globally identify transcript start sites (TSS) that were present during growth on sulfide, biogenic S⁰, and thiosulfate as sole electron donors. TSS positions were used in combination with RNA-seq data from cultures growing on these same electron donors to identify both basal promoter elements and motifs associated with electron donor-dependent transcriptional regulation. These motifs were conserved across homologous Chlorobiaceae promoters. Two lines of evidence suggest that sulfide-mediated repression is the dominant regulatory mode in Cba. tepidum First, motifs associated with genes regulated by sulfide overlap key basal promoter elements. Second, deletion of the Cba. tepidum1277 (CT1277) gene, encoding a putative regulatory protein, leads to constitutive overexpression of the sulfide:quinone oxidoreductase CT1087 in the absence of sulfide. The results suggest that sulfide is the master regulator of sulfur metabolism in Cba. tepidum and the Chlorobiaceae Finally, the identification of basal promoter elements with differing strengths will further the development of synthetic biology in Cba. tepidum and perhaps other ChlorobiaceaeIMPORTANCE Elemental sulfur is a key intermediate in biogeochemical sulfur cycling. The photoautotrophic green sulfur bacterium Chlorobaculum tepidum either produces or consumes elemental sulfur depending on the availability of sulfide in the environment. Our results reveal transcriptional dynamics of Chlorobaculum tepidum on elemental sulfur and increase our understanding of the mechanisms of transcriptional regulation governing growth on different reduced sulfur compounds. This report identifies genes and sequence motifs that likely play significant roles in the production and consumption of elemental sulfur. Beyond this focused impact, this report paves the way for the development of synthetic biology in Chlorobaculum tepidum and other Chlorobiaceae by providing a comprehensive identification of promoter elements for control of gene expression, a key element of strain engineering.