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.

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

2019 ◽  
Vol 14 (1) ◽  
pp. 104-122 ◽  
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

Abstract Most autotrophs use the Calvin–Benson–Bassham (CBB) cycle for carbon fixation. In contrast, 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 may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cycle 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 cycle 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, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment.

scholarly journals Genetic evidence for two carbon fixation pathways in symbiotic and free-living bacteria: The Calvin-Benson-Bassham cycle and the reverse tricarboxylic acid cycle

2018 ◽  
Author(s):  
Maxim Rubin-Blum ◽  
Nicole Dubilier ◽  
Manuel Kleiner
Keyword(s):  
Carbon Fixation ◽  
Tricarboxylic Acid Cycle ◽  
Electron Flow ◽  
Tricarboxylic Acid ◽  
Riftia Pachyptila ◽  
Heterodisulfide Reductase ◽  
Free Living ◽  
Sulfur Oxidizer ◽  
Potential Benefits ◽  
Sulfur Oxidizing

AbstractVery few bacteria are able to fix carbon via both the reverse tricarboxylic acid (rTCA) and the Calvin-Benson-Bassham (CBB) cycles, such as symbiotic, sulfur-oxidizing bacteria that are the sole carbon source for the marine tubeworm Riftia pachyptila, the fastest growing invertebrate. To date, this co-existence of two carbon fixation pathways had not been found in a cultured bacterium and could thus not be studied in detail. Moreover, it was not clear if these two pathways were encoded in the same symbiont individual, or if two symbiont populations, each with one of the pathways, co-existed within tubeworms. With comparative genomics, we show that Thioflavicoccus mobilis, a cultured, free-living gammaproteobacterial sulfur oxidizer, possesses the genes for both carbon fixation pathways. Here, we also show that both the CBB and rTCA pathways are likely encoded in the genome of the sulfur-oxidizing symbiont of the tubeworm Escarpia laminata from deep-sea asphalt volcanoes in the Gulf of Mexico. Finally, we provide genomic and transcriptomic data suggesting a potential electron flow towards the rTCA cycle carboxylase 2-oxoglutarate:ferredoxin oxidoreductase, via a rare variant of NADH dehydrogenase/heterodisulfide reductase. This electron bifurcating complex, together with NAD(P)+ transhydrogenase and Na+ translocating Rnf membrane complexes may improve the efficiency of the rTCA cycle in both the symbiotic and the free-living sulfur oxidizer.ImportancePrimary production on Earth is dependent on autotrophic carbon fixation, which leads to the incorporation of carbon dioxide into biomass. Multiple metabolic pathways have been described for autotrophic carbon fixation, but most autotrophic organisms were assumed to have the genes for only one of these pathways. Our finding of a cultivable bacterium with two carbon fixation pathways in its genome opens the possibility to study the potential benefits of having two pathways and the interplay between these pathways. Additionally, this will allow the investigation of the unusual, and potentially very efficient mechanism of electron flow that could drive the rTCA cycle in these autotrophs. Such studies will deepen our understanding of carbon fixation pathways and could provide new avenues for optimizing carbon fixation in biotechnological applications.

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 Genetic Evidence for Two Carbon Fixation Pathways (the Calvin-Benson-Bassham Cycle and the Reverse Tricarboxylic Acid Cycle) in Symbiotic and Free-Living Bacteria

mSphere ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Maxim Rubin-Blum ◽  
Nicole Dubilier ◽  
Manuel Kleiner
Keyword(s):  
Carbon Fixation ◽  
Tricarboxylic Acid Cycle ◽  
Electron Flow ◽  
Tricarboxylic Acid ◽  
Heterodisulfide Reductase ◽  
Free Living ◽  
Content Type ◽  
Sulfur Oxidizer ◽  
Potential Benefits ◽  
Sulfur Oxidizing

ABSTRACT Very few bacteria are able to fix carbon via both the reverse tricarboxylic acid (rTCA) and the Calvin-Benson-Bassham (CBB) cycles, such as symbiotic, sulfur-oxidizing bacteria that are the sole carbon source for the marine tubeworm Riftia pachyptila, the fastest-growing invertebrate. To date, the coexistence of these two carbon fixation pathways had not been found in a cultured bacterium and could thus not be studied in detail. Moreover, it was not clear if these two pathways were encoded in the same symbiont individual, or if two symbiont populations, each with one of the pathways, coexisted within tubeworms. With comparative genomics, we show that Thioflavicoccus mobilis, a cultured, free-living gammaproteobacterial sulfur oxidizer, possesses the genes for both carbon fixation pathways. Here, we also show that both the CBB and rTCA pathways are likely encoded in the genome of the sulfur-oxidizing symbiont of the tubeworm Escarpia laminata from deep-sea asphalt volcanoes in the Gulf of Mexico. Finally, we provide genomic and transcriptomic data suggesting a potential electron flow toward the rTCA cycle carboxylase 2-oxoglutarate:ferredoxin oxidoreductase, via a rare variant of NADH dehydrogenase/heterodisulfide reductase in the E. laminata symbiont. This electron-bifurcating complex, together with NAD(P)+ transhydrogenase and Na+ translocating Rnf membrane complexes, may improve the efficiency of the rTCA cycle in both the symbiotic and the free-living sulfur oxidizer. IMPORTANCE Primary production on Earth is dependent on autotrophic carbon fixation, which leads to the incorporation of carbon dioxide into biomass. Multiple metabolic pathways have been described for autotrophic carbon fixation, but most autotrophic organisms were assumed to have the genes for only one of these pathways. Our finding of a cultivable bacterium with two carbon fixation pathways in its genome, the rTCA and the CBB cycle, opens the possibility to study the potential benefits of having these two pathways and the interplay between them. Additionally, this will allow the investigation of the unusual and potentially very efficient mechanism of electron flow that could drive the rTCA cycle in these autotrophs. Such studies will deepen our understanding of carbon fixation pathways and could provide new avenues for optimizing carbon fixation in biotechnological applications.

scholarly journals Systems-informed genome mining for electroautotrophic microbial production

2020 ◽  
Author(s):  
Anthony J. Abel ◽  
Jacob M. Hilzinger ◽  
Adam P. Arkin ◽  
Douglas S. Clark
Keyword(s):  
Carbon Fixation ◽  
Microbial Respiration ◽  
Tricarboxylic Acid Cycle ◽  
Genome Mining ◽  
Tricarboxylic Acid ◽  
Nitrate Respiration ◽  
Fixation Rate ◽  
Acid Cycle ◽  
Carbon Molecules ◽  
Reductive Tricarboxylic Acid Cycle

AbstractMicrobial electrosynthesis (MES) systems can store renewable energy and CO2 in many-carbon molecules inaccessible to abiotic electrochemistry. Here, we develop a multiphysics model to investigate the fundamental and practical limits of MES enabled by direct electron uptake and we identify organisms in which this biotechnological CO2-fixation strategy can be realized. Systematic model comparisons of microbial respiration and carbon fixation strategies revealed that, under aerobic conditions, the CO2 fixation rate is limited to <6 μmol/cm2/hr by O2 mass transport despite efficient electron utilization. In contrast, anaerobic nitrate respiration enables CO2 fixation rates >50 μmol/cm2/hr for microbes using the reductive tricarboxylic acid cycle. Phylogenetic analysis, validated by recapitulating experimental demonstrations of electroautotrophy, uncovered multiple probable electroautotrophic organisms and a significant number of genetically tractable strains that require heterologous expression of <5 proteins to gain electroautotrophic function. The model and analysis presented here will guide microbial engineering and reactor design for practical MES systems.

scholarly journals Abundance of Reverse Tricarboxylic Acid Cycle Genes in Free-Living Microorganisms at Deep-Sea Hydrothermal Vents

2004 ◽  
Vol 70 (10) ◽  
pp. 6282-6289 ◽  
Author(s):  
Barbara J. Campbell ◽  
S. Craig Cary
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vents ◽  
Tricarboxylic Acid Cycle ◽  
Calvin Cycle ◽  
Tricarboxylic Acid ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Free Living ◽  
Bisphosphate Carboxylase ◽  
Acid Cycle

ABSTRACT Since the discovery of hydrothermal vents more than 25 years ago, the Calvin-Bassham-Benson (Calvin) cycle has been considered the principal carbon fixation pathway in this microbe-based ecosystem. However, on the basis of recent molecular data of cultured free-living and noncultured episymbiotic members of the epsilon subdivision of Proteobacteria and earlier carbon isotope data of primary consumers, an alternative autotrophic pathway may predominate. Here, genetic and culture-based approaches demonstrated the abundance of reverse tricarboxylic acid cycle genes compared to the abundance of Calvin cycle genes in microbial communities from two geographically distinct deep-sea hydrothermal vents. PCR with degenerate primers for three key genes in the reverse tricarboxylic acid cycle and form I and form II of ribulose 1,5-bisphosphate carboxylase/oxygenase (Calvin cycle marker gene) were utilized to demonstrate the abundance of the reverse tricarboxylic acid cycle genes in diverse vent samples. These genes were also expressed in at least one chimney sample. Diversity, similarity matrix, and phylogenetic analyses of cloned samples and amplified gene products from autotrophic enrichment cultures suggest that the majority of autotrophs that utilize the reverse tricarboxylic acid cycle are members of the epsilon subdivision of Proteobacteria. These results parallel the results of previously published molecular surveys of 16S rRNA genes, demonstrating the dominance of members of the epsilon subdivision of Proteobacteria in free-living hydrothermal vent communities. Members of the epsilon subdivision of Proteobacteria are also ubiquitous in many other microaerophilic to anaerobic sulfidic environments, such as the deep subsurface. Therefore, the reverse tricarboxylic acid cycle may be a major autotrophic pathway in these environments and significantly contribute to global autotrophic processes.

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 Sulfur-Oxidizing Symbionts without Canonical Genes for Autotrophic CO2Fixation

mBio ◽  
2019 ◽  
Vol 10 (3) ◽  
Author(s):  
Brandon K. B. Seah ◽  
Chakkiath Paul Antony ◽  
Bruno Huettel ◽  
Jan Zarzycki ◽  
Lennart Schada von Borzyskowski ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Food Source ◽  
Carbon Fixation ◽  
Tricarboxylic Acid Cycle ◽  
Carbon Sources ◽  
Coastal Sediments ◽  
Carbon Stable Isotope ◽  
Main Food ◽  
Sulfur Oxidizing ◽  
Main Food Source

ABSTRACTSince the discovery of symbioses between sulfur-oxidizing (thiotrophic) bacteria and invertebrates at hydrothermal vents over 40 years ago, it has been assumed that autotrophic fixation of CO2by the symbionts drives these nutritional associations. In this study, we investigated “CandidatusKentron,” the clade of symbionts hosted byKentrophoros, a diverse genus of ciliates which are found in marine coastal sediments around the world. Despite being the main food source for their hosts, Kentron bacteria lack the key canonical genes for any of the known pathways for autotrophic carbon fixation and have a carbon stable isotope fingerprint that is unlike other thiotrophic symbionts from similar habitats. Our genomic and transcriptomic analyses instead found metabolic features consistent with growth on organic carbon, especially organic and amino acids, for which they have abundant uptake transporters. All known thiotrophic symbionts have converged on using reduced sulfur to gain energy lithotrophically, but they are diverse in their carbon sources. Some clades are obligate autotrophs, while many are mixotrophs that can supplement autotrophic carbon fixation with heterotrophic capabilities similar to those in Kentron. Here we show that Kentron bacteria are the only thiotrophic symbionts that appear to be entirely heterotrophic, unlike all other thiotrophic symbionts studied to date, which possess either the Calvin-Benson-Bassham or the reverse tricarboxylic acid cycle for autotrophy.IMPORTANCEMany animals and protists depend on symbiotic sulfur-oxidizing bacteria as their main food source. These bacteria use energy from oxidizing inorganic sulfur compounds to make biomass autotrophically from CO2, serving as primary producers for their hosts. Here we describe a clade of nonautotrophic sulfur-oxidizing symbionts, “CandidatusKentron,” associated with marine ciliates. They lack genes for known autotrophic pathways and have a carbon stable isotope fingerprint heavier than other symbionts from similar habitats. Instead, they have the potential to oxidize sulfur to fuel the uptake of organic compounds for heterotrophic growth, a metabolic mode called chemolithoheterotrophy that is not found in other symbioses. Although several symbionts have heterotrophic features to supplement primary production, in Kentron they appear to supplant it entirely.

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