scholarly journals Comparative Genome Analysis of the Genus Thiothrix Involving Three Novel Species, Thiothrix subterranea sp. nov. Ku-5, Thiothrix litoralis sp. nov. AS and “Candidatus Thiothrix anitrata” sp. nov. A52, Revealed the Conservation of the Pathways of Dissimilatory Sulfur Metabolism and Variations in the Genetic Inventory for Nitrogen Metabolism and Autotrophic Carbon Fixation

2021 ◽  
Vol 12 ◽  
Author(s):  
Nikolai V. Ravin ◽  
Tatyana S. Rudenko ◽  
Dmitry D. Smolyakov ◽  
Alexey V. Beletsky ◽  
Andrey L. Rakitin ◽  
...  
Keyword(s):  
Core Genome ◽  
Carbon Fixation ◽  
Tricarboxylic Acid Cycle ◽  
Sulfur Metabolism ◽  
Sulfide Oxidation ◽  
Calvin Cycle ◽  
Sulfur Oxidation ◽  
Rrna Gene ◽  
Reduced Sulfur Compounds ◽  
Hybridization Data

Two strains of filamentous, colorless sulfur bacteria were isolated from bacterial fouling in the outflow of hydrogen sulfide-containing waters from a coal mine (Thiothrix sp. Ku-5) and on the seashore of the White Sea (Thiothrix sp. AS). Metagenome-assembled genome (MAG) A52 was obtained from a sulfidic spring in the Volgograd region, Russia. Phylogenetic analysis based on the 16S rRNA gene sequences showed that all genomes represented the genus Thiothrix. Based on their average nucleotide identity and digital DNA-DNA hybridization data these new isolates and the MAG represent three species within the genus Thiothrix with the proposed names Thiothrix subterranea sp. nov. Ku-5T, Thiothrix litoralis sp. nov. AST, and “Candidatus Thiothrix anitrata” sp. nov. A52. The complete genome sequences of Thiothrix fructosivorans QT and Thiothrix unzii A1T were determined. Complete genomes of seven Thiothrix isolates, as well as two MAGs, were used for pangenome analysis. The Thiothrix core genome consisted of 1,355 genes, including ones for the glycolysis, the tricarboxylic acid cycle, the aerobic respiratory chain, and the Calvin cycle of carbon fixation. Genes for dissimilatory oxidation of reduced sulfur compounds, namely the branched SOX system (SoxAXBYZ), direct (soeABC) and indirect (aprAB, sat) pathways of sulfite oxidation, sulfur oxidation complex Dsr (dsrABEFHCEMKLJONR), sulfide oxidation systems SQR (sqrA, sqrF), and FCSD (fccAB) were found in the core genome. Genomes differ in the set of genes for dissimilatory reduction of nitrogen compounds, nitrogen fixation, and the presence of various types of RuBisCO.

scholarly journals Genomic and Metabolic Insights into Two Novel Thiothrix Species from Enhanced Biological Phosphorus Removal Systems

2020 ◽  
Vol 8 (12) ◽  
pp. 2030
Author(s):  
Andrey V. Mardanov ◽  
Eugeny V. Gruzdev ◽  
Dmitry D. Smolyakov ◽  
Tatyana S. Rudenko ◽  
Alexey V. Beletsky ◽  
...  
Keyword(s):  
Phosphorus Removal ◽  
Tricarboxylic Acid Cycle ◽  
Sulfide Oxidation ◽  
Sulfur Oxidation ◽  
Co2 Assimilation ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Enhanced Biological Phosphorus Removal ◽  
Biological Phosphorus Removal ◽  
Biological Phosphorus

Two metagenome-assembled genomes (MAGs), obtained from laboratory-scale enhanced biological phosphorus removal bioreactors, were analyzed. The values of 16S rRNA gene sequence identity, average nucleotide identity, and average amino acid identity indicated that these genomes, designated as RT and SSD2, represented two novel species within the genus Thiothrix, ‘Candidatus Thiothrix moscowensis’ and ‘Candidatus Thiothrix singaporensis’. A complete set of genes for the tricarboxylic acid cycle and electron transport chain indicates a respiratory type of metabolism. A notable feature of RT and SSD2, as well as other Thiothrix species, is the presence of a flavin adenine dinucleotide (FAD)-dependent malate:quinone oxidoreductase instead of nicotinamide adenine dinucleotide (NAD)-dependent malate dehydrogenase. Both MAGs contained genes for CO2 assimilation through the Calvin–Benson–Bassam cycle; sulfide oxidation (sqr, fccAB), sulfur oxidation (rDsr complex), direct (soeABC) and indirect (aprBA, sat) sulfite oxidation, and the branched Sox pathway (SoxAXBYZ) of thiosulfate oxidation to sulfur and sulfate. All these features indicate a chemoorganoheterotrophic, chemolithoautotrophic, and chemolithoheterotrophic lifestyle. Both MAGs comprise genes for nitrate reductase and NO-reductase, while SSD2 also contains genes for nitrite reductase. The presence of polyphosphate kinase and exopolyphosphatase suggests that RT and SSD2 could accumulate and degrade polyhosphates during the oxic-anoxic growth cycle in the bioreactors, such as typical phosphate-accumulating microorganisms.

scholarly journals Evidence for Autotrophic CO2 Fixation via the Reductive Tricarboxylic Acid Cycle by Members of the ε Subdivision of Proteobacteria

2005 ◽  
Vol 187 (9) ◽  
pp. 3020-3027 ◽  
Author(s):  
Michael Hügler ◽  
Carl O. Wirsen ◽  
Georg Fuchs ◽  
Craig D. Taylor ◽  
Stefan M. Sievert
Keyword(s):  
Carbon Fixation ◽  
Tricarboxylic Acid Cycle ◽  
Calvin Cycle ◽  
Tricarboxylic Acid ◽  
Rrna Gene ◽  
Atp Citrate Lyase ◽  
Acid Cycle ◽  
Key Enzymes ◽  
Citrate Lyase ◽  
Reductive Tricarboxylic Acid Cycle

ABSTRACT Based on 16S rRNA gene surveys, bacteria of the ε subdivision of proteobacteria have been identified to be important members of microbial communities in a variety of environments, and quite a few have been demonstrated to grow autotrophically. However, no information exists on what pathway of autotrophic carbon fixation these bacteria might use. In this study, Thiomicrospira denitrificans and Candidatus Arcobacter sulfidicus, two chemolithoautotrophic sulfur oxidizers of the ε subdivision of proteobacteria, were examined for activities of the key enzymes of the known autotrophic CO2 fixation pathways. Both organisms contained activities of the key enzymes of the reductive tricarboxylic acid cycle, ATP citrate lyase, 2-oxoglutarate:ferredoxin oxidoreductase, and pyruvate:ferredoxin oxidoreductase. Furthermore, no activities of key enzymes of other CO2 fixation pathways, such as the Calvin cycle, the reductive acetyl coenzyme A pathway, and the 3-hydroxypropionate cycle, could be detected. In addition to the key enzymes, the activities of the other enzymes involved in the reductive tricarboxylic acid cycle could be measured. Sections of the genes encoding the α- and β-subunits of ATP citrate lyase could be amplified from both organisms. These findings represent the first direct evidence for the operation of the reductive tricarboxylic acid cycle for autotrophic CO2 fixation in ε-proteobacteria. Since ε-proteobacteria closely related to these two organisms are important in many habitats, such as hydrothermal vents, oxic-sulfidic interfaces, or oilfields, these results suggest that autotrophic CO2 fixation via the reductive tricarboxylic acid cycle might be more important than previously considered.

scholarly journals A Comparative Quantitative Proteomic Study Identifies New Proteins Relevant for Sulfur Oxidation in the Purple Sulfur Bacterium Allochromatium vinosum

2014 ◽  
Vol 80 (7) ◽  
pp. 2279-2292 ◽  
Author(s):  
Thomas Weissgerber ◽  
Marc Sylvester ◽  
Lena Kröninger ◽  
Christiane Dahl
Keyword(s):  
Sulfur Metabolism ◽  
Sulfur Oxidation ◽  
Hypothetical Protein ◽  
Mrna Levels ◽  
Reduced Sulfur Compounds ◽  
Allochromatium Vinosum ◽  
Purple Sulfur Bacterium ◽  
Content Type ◽  
Protein Levels ◽  
New Genes

ABSTRACTIn the present study, we compared the proteome response ofAllochromatium vinosumwhen growing photoautotrophically in the presence of sulfide, thiosulfate, and elemental sulfur with the proteome response when the organism was growing photoheterotrophically on malate. Applying tandem mass tag analysis as well as two-dimensional (2D) PAGE, we detected 1,955 of the 3,302 predicted proteins by identification of at least two peptides (59.2%) and quantified 1,848 of the identified proteins. Altered relative protein amounts (≥1.5-fold) were observed for 385 proteins, corresponding to 20.8% of the quantifiedA. vinosumproteome. A significant number of the proteins exhibiting strongly enhanced relative protein levels in the presence of reduced sulfur compounds are well documented essential players during oxidative sulfur metabolism, e.g., the dissimilatory sulfite reductase DsrAB. Changes in protein levels generally matched those observed for the respective relative mRNA levels in a previous study and allowed identification of new genes/proteins participating in oxidative sulfur metabolism. One gene cluster (hyd; Alvin_2036-Alvin_2040) and one hypothetical protein (Alvin_2107) exhibiting strong responses on both the transcriptome and proteome levels were chosen for gene inactivation and phenotypic analyses of the respective mutant strains, which verified the importance of the so-called Isp hydrogenase supercomplex for efficient oxidation of sulfide and a crucial role of Alvin_2107 for the oxidation of sulfur stored in sulfur globules to sulfite. In addition, we analyzed the sulfur globule proteome and identified a new sulfur globule protein (SgpD; Alvin_2515).

scholarly journals Molecular Characterization of the Diversity and Distribution of a Thermal Spring Microbial Community by Using rRNA and Metabolic Genes

2008 ◽  
Vol 74 (15) ◽  
pp. 4910-4922 ◽  
Author(s):  
Justine R. Hall ◽  
Kendra R. Mitchell ◽  
Olan Jackson-Weaver ◽  
Ara S. Kooser ◽  
Brandi R. Cron ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
16S Rrna ◽  
Hot Spring ◽  
Sulfide Oxidation ◽  
Calvin Cycle ◽  
Thermal Spring ◽  
Nitrite Reduction ◽  
Rrna Gene ◽  
Bacterial Gene ◽  
Metabolic Genes

ABSTRACT The diversity and distribution of a bacterial community from Coffee Pots Hot Spring, a thermal spring in Yellowstone National Park with a temperature range of 39.3 to 74.1°C and pH range of 5.75 to 6.91, were investigated by sequencing cloned PCR products and quantitative PCR (qPCR) of 16S rRNA and metabolic genes. The spring was inhabited by three Aquificae genera—Thermocrinis, Hydrogenobaculum, and Sulfurihydrogenibium—and members of the Alpha-, Beta-, and Gammaproteobacteria, Firmicutes, Acidobacteria, Deinococcus-Thermus, and candidate division OP5. The in situ chemical affinities were calculated for 41 potential metabolic reactions using measured environmental parameters and a range of hydrogen and oxygen concentrations. Reactions that use oxygen, ferric iron, sulfur, and nitrate as electron acceptors were predicted to be the most energetically favorable, while reactions using sulfate were expected to be less favorable. Samples were screened for genes used in ammonia oxidation (amoA, bacterial gene only), the reductive tricarboxylic acid (rTCA) cycle (aclB), the Calvin cycle (cbbM), sulfate reduction (dsrAB), nitrogen fixation (nifH), nitrite reduction (nirK), and sulfide oxidation (soxEF1) by PCR. Genes for carbon fixation by the rTCA cycle and nitrogen fixation were detected. All aclB sequences were phylogenetically related and spatially correlated to Sulfurihydrogenibium 16S rRNA gene sequences using qPCR (R 2 = 0.99). This result supports the recent finding of citrate cleavage by enzymes other than ATP citrate lyase in the rTCA cycle of the Aquificaceae family. We briefly consider potential biochemical mechanisms that may allow Sulfurihydrogenibium and Thermocrinis to codominate some hydrothermal environments.

scholarly journals Physiological Proteomics of the Uncultured Endosymbiont of Riftia pachyptila

Science ◽  
2007 ◽  
Vol 315 (5809) ◽  
pp. 247-250 ◽  
Author(s):  
Stephanie Markert ◽  
Cordelia Arndt ◽  
Horst Felbeck ◽  
Dörte Becher ◽  
Stefan M. Sievert ◽  
...  
Keyword(s):  
Deep Sea ◽  
Tricarboxylic Acid Cycle ◽  
Sulfide Oxidation ◽  
Calvin Cycle ◽  
Tricarboxylic Acid ◽  
Riftia Pachyptila ◽  
Proteomic Approach ◽  
Reductive Tricarboxylic Acid Cycle ◽  
Metagenome Sequence

The bacterial endosymbiont of the deep-sea tube worm Riftia pachyptila has never been successfully cultivated outside its host. In the absence of cultivation data, we have taken a proteomic approach based on the metagenome sequence to study the metabolism of this peculiar microorganism in detail. As one result, we found that three major sulfide oxidation proteins constitute ∼12% of the total cytosolic proteome, which highlights the essential role of these enzymes for the symbiont's energy metabolism. Unexpectedly, the symbiont uses the reductive tricarboxylic acid cycle in addition to the previously identified Calvin cycle for CO2 fixation.

scholarly journals Evidence for Niche Partitioning Revealed by the Distribution of Sulfur Oxidation Genes Collected from Areas of a Terrestrial Sulfidic Spring with Differing Geochemical Conditions

2012 ◽  
Vol 79 (4) ◽  
pp. 1171-1182 ◽  
Author(s):  
Brendan Headd ◽  
Annette Summers Engel
Keyword(s):  
Gene Sequence ◽  
Sulfide Oxidation ◽  
Niche Partitioning ◽  
Sulfur Oxidation ◽  
Reduced Sulfur Compounds ◽  
Content Type ◽  
Geochemical Conditions ◽  
Sequence Variations ◽  
Bacterial Genes ◽  
Outflow Channel

ABSTRACTThe diversity and phylogenetic significance of bacterial genes in the environment has been well studied, but comparatively little attention has been devoted to understanding the functional significance of different variations of the same metabolic gene that occur in the same environment. We analyzed the geographic distribution of 16S rRNA pyrosequences andsoxBgenes along a geochemical gradient in a terrestrial sulfidic spring to identify how different taxonomic variations of thesoxBgene were naturally distributed within the spring outflow channel and to identify possible evidence for altered SoxB enzyme function in nature. Distinct compositional differences between bacteria that utilize their SoxB enzyme in theParacoccussulfide oxidation pathway (e.g.,Bradyrhizobium,Paracoccus, andRhodovulum) and bacteria that utilize their SoxB enzyme in the branched pathway (e.g.,Chlorobium,Thiothrix,Thiobacillus,Halothiobacillus, andThiomonas) were identified. Different variations of thesoxBgenes were present at different locations within the spring outflow channel in a manner that significantly corresponded to geochemical conditions. The distribution of the differentsoxBgene sequence variations suggests that the enzymes encoded by these genes are functionally different and could be optimized to specific geochemical conditions that define niche space for bacteria capable of oxidizing reduced sulfur compounds.

scholarly journals The Genome Sequence of the Metal-Mobilizing, Extremely Thermoacidophilic Archaeon Metallosphaera sedula Provides Insights into Bioleaching-Associated Metabolism

2007 ◽  
Vol 74 (3) ◽  
pp. 682-692 ◽  
Author(s):  
Kathryne S. Auernik ◽  
Yukari Maezato ◽  
Paul H. Blum ◽  
Robert M. Kelly
Keyword(s):  
Genome Sequence ◽  
Carbon Fixation ◽  
Metal Tolerance ◽  
Sulfur Metabolism ◽  
Sulfide Oxidation ◽  
Iron Oxidation ◽  
Metal Sulfide ◽  
Response Analysis ◽  
Terminal Oxidase ◽  
Metallosphaera Sedula

ABSTRACT Despite their taxonomic description, not all members of the order Sulfolobales are capable of oxidizing reduced sulfur species, which, in addition to iron oxidation, is a desirable trait of biomining microorganisms. However, the complete genome sequence of the extremely thermoacidophilic archaeon Metallosphaera sedula DSM 5348 (2.2 Mb, ∼2,300 open reading frames [ORFs]) provides insights into biologically catalyzed metal sulfide oxidation. Comparative genomics was used to identify pathways and proteins involved (directly or indirectly) with bioleaching. As expected, the M. sedula genome contains genes related to autotrophic carbon fixation, metal tolerance, and adhesion. Also, terminal oxidase cluster organization indicates the presence of hybrid quinol-cytochrome oxidase complexes. Comparisons with the mesophilic biomining bacterium Acidithiobacillus ferrooxidans ATCC 23270 indicate that the M. sedula genome encodes at least one putative rusticyanin, involved in iron oxidation, and a putative tetrathionate hydrolase, implicated in sulfur oxidation. The fox gene cluster, involved in iron oxidation in the thermoacidophilic archaeon Sulfolobus metallicus, was also identified. These iron- and sulfur-oxidizing components are missing from genomes of nonleaching members of the Sulfolobales, such as Sulfolobus solfataricus P2 and Sulfolobus acidocaldarius DSM 639. Whole-genome transcriptional response analysis showed that 88 ORFs were up-regulated twofold or more in M. sedula upon addition of ferrous sulfate to yeast extract-based medium; these included genes for components of terminal oxidase clusters predicted to be involved with iron oxidation, as well as genes predicted to be involved with sulfur metabolism. Many hypothetical proteins were also differentially transcribed, indicating that aspects of the iron and sulfur metabolism of M. sedula remain to be identified and characterized.

scholarly journals Reconciling a Model of Core Metabolism with Growth Yield Predicts Biochemical Mechanisms and Efficiency for a Versatile Chemoautotroph

2019 ◽  
Author(s):  
Jesse McNichol ◽  
Stefan M. Sievert
Keyword(s):  
Comparative Genomics ◽  
Energy Conservation ◽  
Carbon Fixation ◽  
Tricarboxylic Acid Cycle ◽  
Conceptual Modeling ◽  
Growth Yield ◽  
Sulfur Oxidation ◽  
Growth Efficiency ◽  
Biochemical Mechanisms ◽  
Core Metabolism

AbstractObligately chemoautotrophic Campylobacteria dominate productivity in dark, sulfidic, and oxygen-depleted environments. However, biochemical mechanisms underlying their growth remain poorly known, limiting understanding of their physiology, ecology, and biogeochemical impact. In this study, we used comparative genomics, conceptual modeling of core metabolism, and chemostat growth yields to derive a model of energy conservation consistent with experimental data for the versatile chemoautotroph Sulfurimonas denitrificans. Our model rests on three core mechanisms: Firstly, to allow electrogenic sulfur-based denitrification, we predict that the campylobacterial-type sulfur oxidation enzyme complex must donate electrons to the membrane quinone pool, possibly via a sulfide:quinone oxidoreductase. Secondly, to account for the unexpectedly low growth efficiency of aerobic sulfur oxidation compared to denitrification, we posit the high-affinity campylobacterial-type cbb3 cytochrome c oxidase has a relatively low H+/e− of 1, likely due to a lack of proton pumping under physiological conditions. Thirdly, we hypothesize that reductant for carbon fixation by the reverse tricarboxylic acid cycle is produced by a non-canonical complex I that reduces both ferredoxin and NAD(P)H. This complex is conserved among related Campylobacteria and may have allowed for the radiation of organisms like S. denitrificans into sulfur-rich environments that became available after the great oxidation event. Our theoretical model has two major implications. Firstly, it sets the stage for future experimental work by providing testable hypotheses about the physiology, biochemistry, and evolution of chemoautotrophic Campylobacteria. Secondly, it provides constraints on the carbon fixation potential of chemoautotrophic Campylobacteria in sulfidic environments worldwide by predicting theoretical ranges of chemosynthetic growth efficiency.SignificanceChemoautotrophic Campylobacteria are abundant in many low-oxygen, high-sulfide environments where they contribute significantly to dark carbon fixation. Although the overall redox reactions they catalyze are known, the specific biochemical mechanisms that support their growth are mostly unknown. Our study combines conceptual modeling of core metabolic pathways, comparative genomics, and measurements of physiological growth yield in a chemostat to infer the most likely mechanisms of chemoautotrophic energy conservation in the model organism Sulfurimonas denitrificans. The hypotheses proposed herein are novel, experimentally falsifiable, and will guide future biochemical, physiological, and environmental modelling studies. Ultimately, investigating the core mechanisms of energy conservation will help us better understand the evolution and physiological diversification of chemoautotrophic Campylobacteria and their role in modern ecosystems.

scholarly journals Physiology, Taxonomy, and Sulfur Metabolism of the Sulfolobales, an Order of Thermoacidophilic Archaea

2021 ◽  
Vol 12 ◽  
Author(s):  
Li-Jun Liu ◽  
Zhen Jiang ◽  
Pei Wang ◽  
Ya-Ling Qin ◽  
Wen Xu ◽  
...  
Keyword(s):  
Current Knowledge ◽  
Sulfur Metabolism ◽  
Sulfide Oxidation ◽  
Sulfur Oxidation ◽  
Physiological Characteristic ◽  
Thermoacidophilic Archaea ◽  
Sulfite Oxidation ◽  
Code Of Nomenclature ◽  
Future Challenges ◽  
Sulfur Trafficking

The order Sulfolobales (phylum Crenarchaeota) is a group of thermoacidophilic archaea. The first member of the Sulfolobales was discovered in 1972, and current 23 species are validly named under the International Code of Nomenclature of Prokaryotes. The majority of members of the Sulfolobales is obligately or facultatively chemolithoautotrophic. When they grow autotrophically, elemental sulfur or reduced inorganic sulfur compounds are their energy sources. Therefore, sulfur metabolism is the most important physiological characteristic of the Sulfolobales. The functions of some enzymes and proteins involved in sulfur reduction, sulfur oxidation, sulfide oxidation, thiosulfate oxidation, sulfite oxidation, tetrathionate hydrolysis, and sulfur trafficking have been determined. In this review, we describe current knowledge about the physiology, taxonomy, and sulfur metabolism of the Sulfolobales, and note future challenges in this field.

scholarly journals Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)

2018 ◽  
Author(s):  
Adrien Assié ◽  
Nikolaus Leisch ◽  
Dimitri V. Meier ◽  
Harald Gruber-Vodicka ◽  
Halina E. Tegetmeyer ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Carbon Fixation ◽  
Tricarboxylic Acid Cycle ◽  
Calvin Cycle ◽  
Tricarboxylic Acid ◽  
Multiple Sources ◽  
Free Living ◽  
Sulfur Oxidizing ◽  
Reductive Tricarboxylic Acid Cycle ◽  
Horizontal Acquisition

AbstractAlthough the majority of known autotrophs use the Calvin-Benson-Bassham (CBB) cycle for carbon fixation, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts (“Candidatus Thiobarba”) of deep-sea mussels that have acquired a complete CBB cycle and lost key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB genes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that “Ca. Thiobarba” switched from the rTCA to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated “Ca. Thiobarba”. Direct stable isotope fingerprinting showed that “Ca. Thiobarba” has typical CBB signatures, additional evidence that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways across the tree of life, and the interpretation of stable isotope measurements in the environment.

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