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Clostridium acetobutylicum-Clostridium ljungdahlii Syntrophic Fusion Coculture

Community ID CommunityMech:000336
Ecological State ENGINEERED
Environment static anaerobic laboratory coculture in loosened screw-cap bottles — ontology label: laboratory environment
ENVO:01001405 · HabitatMech ↗

A defined two-member anaerobic coculture of the solventogen Clostridium acetobutylicum ATCC 824 and the acetogen Clostridium ljungdahlii DSM 13528. CO2 and H2 produced by C. acetobutylicum feed C. ljungdahlii, and the pairing also produces interspecies cell fusion with large-scale exchange of protein, RNA, and DNA between the two organisms. RNA sequencing of the coculture against the two monocultures, and of membrane-separated against unseparated cocultures in a transwell system, separates the effect of soluble signals from the effect of direct cell-to-cell contact. The transcriptional program shows differential regulation of the C. ljungdahlii Wood-Ljungdahl pathway and of the motility machinery, and of amino-acid biosynthesis and degradation; arginine and histidine made by C. acetobutylicum are proposed to be metabolized by C. ljungdahlii for extra ATP and carbon. The authors read the pairing as mutualistic rather than the commensalism previously assumed. This record is scoped to the WILD-TYPE pairing. The same laboratory has since reported much higher isopropanol and butanol titers from the same species pair using genetically modified C. acetobutylicum; those are properties of the engineered pairing and are deliberately not curated here.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Clostridium acetobutylicum NCBITaxon:1488 · TaxonMech · TraitMech
PRIMARY_DEGRADER CROSS_FEEDER SYNTROPHIC_PARTNER
DOMINANT
  • PMID:40298437 - SUPPORT (IN_VITRO)
    "Monocultures of C. acetobutylicum ATCC 824 and C. ljungdahlii DSM 13528 as well as cocultures combining the species were grown for RNA extraction"
  • PMID:40298437 - SUPPORT (IN_VITRO)
    "CO2 and H2 produced by the former feed the latter"
  • PMID:40298437 - SUPPORT (IN_VITRO)
    "C. ljungdahlii represents approximately 25% of the coculture population"
Clostridium ljungdahlii NCBITaxon:1538 · TaxonMech · TraitMech
PRIMARY_PRODUCER CROSS_FEEDER SYNTROPHIC_PARTNER
ABUNDANT
  • PMID:40298437 - SUPPORT (IN_VITRO)
    "Monocultures of C. acetobutylicum ATCC 824 and C. ljungdahlii DSM 13528 as well as cocultures combining the species were grown for RNA extraction"
  • PMID:40298437 - SUPPORT (IN_VITRO)
    "autotrophic Wood-Ljungdahl pathway metabolism and genes of the motility machinery"
  • PMID:40298437 - SUPPORT (IN_VITRO)
    "C. ljungdahlii represents approximately 25% of the coculture population"

Ecological Interactions

The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.

Ecological interaction network for Clostridium acetobutylicum-Clostridium ljungdahlii Syntrophic Fusion Coculture Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for cross-feeding. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
Taxon
Cross-feeding
Other

Gas syntrophy - CO2 and H2 transfer to the acetogen

CROSS_FEEDING

C. acetobutylicum releases CO2 and H2 during glucose catabolism, supporting C. ljungdahlii through the Wood-Ljungdahl pathway. Retain CROSS_FEEDING for this reported gas transfer without resolving the broader syntrophy enum question (#752). The monoculture controls used different substrate and gas conditions; their inclusion does not demonstrate facultative cooperation under identical conditions.

Source Taxon: Clostridium acetobutylicum

Target Taxon: Clostridium ljungdahlii

Metabolites: carbon dioxide (CHEBI:16526 · MediaIngredientMech · CMMMech), hydrogen (CHEBI:18276 · MediaIngredientMech · CMMMech)

Biological Processes:

Downstream Effects:
→ Proposed hydrogenase feedback relief through hydrogen removal

HYPOTHESIZED - acetogenic consumption of partner-derived H2 could relieve local hydrogenase feedback in C. acetobutylicum. Early glucose-consumption comparisons are consistent with this reciprocal effect, but do not directly measure hydrogenase activity or isolate local H2 removal.

Evidence

  • PMID:40298437 - SUPPORT (IN_VITRO)
    "CO2 and H2 produced by the former feed the latter"
  • PMID:30391511 - SUPPORT (IN_VITRO)
    "ljungdahlii which fixes CO2, achieved carbon recoveries into C2-C4 alcohols"

Arginine cross-feeding to the acetogen

CROSS_FEEDING

PARTIAL - coculture arginine-biosynthesis and arginine-deiminase expression, together with measured supernatant amino-acid profiles, support proposed C. acetobutylicum-to-C. ljungdahlii cross-feeding. Arginine supplementation increased growth of autotrophic C. ljungdahlii monocultures; it was not a donor-to-recipient flux experiment. HYPOTHESIZED - arginine catabolism supplies additional ATP in coculture. The supplementation response must not be confused with a measured coculture transfer rate or ATP-mediated effect.

Source Taxon: Clostridium acetobutylicum

Target Taxon: Clostridium ljungdahlii

Metabolites: L-arginine (CHEBI:16467 · MediaIngredientMech · CMMMech)

Biological Processes:

Evidence

  • PMID:40298437 - PARTIAL (IN_VITRO)
    "C. ljungdahlii may utilize arginine produced by C. acetobutylicum for additional ATP production"
  • PMID:40298437 - SUPPORT (IN_VITRO)
    "C. acetobutylicum does not have homologs for the arginine deiminase pathway"
  • PMID:40298437 - SUPPORT (IN_VITRO)
    "arginine addition significantly boosted the growth rate and total biomass accumulation"

Histidine degradation feeding the acetogen

CROSS_FEEDING

PARTIAL - histidine-degradation genes in C. ljungdahlii were upregulated early in coculture, and supernatant amino-acid profiles were measured. Histidine supplementation increased autotrophic C. ljungdahlii monoculture growth with acetate and ammonia measurements. HYPOTHESIZED - C. acetobutylicum-derived histidine is transferred to the acetogen and degraded through glutamate and a tetrahydrofolate intermediate that feeds the Wood-Ljungdahl pathway. Supplementation and transcription support this model, but do not directly trace donor-derived carbon through the proposed coculture route.

Source Taxon: Clostridium acetobutylicum

Target Taxon: Clostridium ljungdahlii

Metabolites: L-histidine (CHEBI:15971 · MediaIngredientMech · CMMMech), L-glutamate (CHEBI:29985 · MediaIngredientMech · CMMMech)

Biological Processes:

Evidence

  • PMID:40298437 - PARTIAL (IN_VITRO)
    "four genes involved in histidine degradation to glutamate (CLJU_c21460-21480, 21500) were strongly upregulated early in coculture"
  • PMID:40298437 - PARTIAL (IN_VITRO)
    "we also identified differential regulation of biosynthetic genes of several amino acids, and notably of arginine and histidine"
  • PMID:40298437 - PARTIAL (IN_VITRO)
    "histidine was superior both for increasing growth and CO2 fixation"

Proposed hydrogenase feedback relief through hydrogen removal

PARTIAL - early glucose-consumption rates in coculture were as high as or higher than C. acetobutylicum monocultures under N2 and higher than controls under 80% H2/20% CO2 during the first six hours. The small difference was consistent across three biological replicates. HYPOTHESIZED - local H2 consumption by C. ljungdahlii relieves feedback inhibition of the solventogen hydrogenase. This is a glucose-consumption comparison, not a direct hydrogenase assay or a quantified reciprocal fitness effect.

Source Taxon: Clostridium ljungdahlii

Target Taxon: Clostridium acetobutylicum

Metabolites: hydrogen (CHEBI:18276 · MediaIngredientMech · CMMMech)

Evidence

  • PMID:40298437 - PARTIAL (IN_VITRO)
    "consumption of H2 by C. ljungdahlii would relieve feedback inhibition of C. acetobutylicum"
  • PMID:40298437 - SUPPORT (IN_VITRO)
    "The effect was small, but was present in all three biological replicates"
  • PMID:40298437 - PARTIAL (IN_VITRO)
    "paint a more complex syntrophic picture and suggest a mutualistic relationship"

Contact-associated transcriptional response and proposed growth stimulation

PARTIAL - removing the 0.4 micrometer transwell membrane altered expression, with ribosomal-protein genes in C. acetobutylicum and pyrimidine-biosynthesis genes in C. ljungdahlii enriched among strongly upregulated genes. HYPOTHESIZED - these contact-associated transcriptional patterns indicate growth stimulation of both partners. They are not direct species-specific growth-rate measurements, and the comparison does not isolate cell fusion from other consequences of contact.

Participating Taxa: Clostridium acetobutylicum, Clostridium ljungdahlii

Biological Processes:

Evidence

  • PMID:40298437 - PARTIAL (IN_VITRO)
    "suggests that direct cell-to-cell contact stimulates cell growth of both organisms"
  • PMID:40298437 - SUPPORT (IN_VITRO)
    "separated by a permeable membrane (0.4 µm pore size)"

Proposed amino-acid competition and product inhibition

HYPOTHESIZED - depletion of shared yeast-extract amino acids and accumulation of butyrate and butanol could contribute to the C. ljungdahlii transcriptional survival response. Amino-acid and metabolite profiles provide context, but the study does not isolate nutrient competition from product inhibition or other coculture effects, and does not measure reciprocal harm required for categorical competition.

Source Taxon: Clostridium acetobutylicum

Target Taxon: Clostridium ljungdahlii

Metabolites: butyrate (CHEBI:17968 · MediaIngredientMech · CMMMech), butanol (CHEBI:28885 · MediaIngredientMech · CMMMech)

Evidence

  • PMID:40298437 - PARTIAL (IN_VITRO)
    "inhibitory metabolites (such as butyrate and butanol) and competition for yeast-extract amino acids from the dominating C. acetobutylicum drive C. ljungdahlii to adopt a survival strategy"

Interspecies cell fusion and cytoplasmic material exchange

Wild-type electron microscopy and tomography demonstrate interspecies cell-wall and membrane fusion. The 2020 study also reports protein-dye exchange in the wild-type pairing. Its RNA-label experiment instead pairs wild-type C. ljungdahlii with a C. acetobutylicum-Halo reporter; this supports related-system RNA transfer, not an unmodified-pair RNA assay. DNA integration in the 2024 plasmid-donor experiment is outside this wild-type graph. Fusion remains untyped because structure and exchange do not by themselves establish a fitness sign (#749).

Participating Taxa: Clostridium acetobutylicum, Clostridium ljungdahlii

Biological Processes:

Downstream Effects:
→ Coculture isopropanol and 2,3-butanediol production

HYPOTHESIZED - fusion-associated cytoplasmic exchange could enable the altered metabolite production observed in mixed coculture. Membrane-separation results support contact dependence, but do not selectively perturb fusion or demonstrate that fusion alone causes the product phenotype.

Evidence

  • PMID:32873766 - SUPPORT (IN_VITRO)
    "transmission electron microscopy and electron tomography demonstrated cell wall and membrane fusions between the two organisms"
  • PMID:32873766 - SUPPORT (IN_VITRO)
    "transport of green-tagged C. acetobutylicum proteins into C. ljungdahlii"
  • PMID:32873766 - PARTIAL (IN_VITRO)
    "C. ljungdahlii cells with labeled RNA were cocultured with the C. acetobutylicum-Halo strain"

Coculture isopropanol and 2,3-butanediol production

The wild-type coculture produced isopropanol and 2,3-butanediol under the founding study conditions, whereas its reported monoculture controls did not. This is condition-specific emergence: the 2020 primary account explicitly notes that C. ljungdahlii can in principle produce 2,3-butanediol alone. Contact-associated material exchange is a proposed explanation, not a fusion-specific causal intervention. The product phenotype remains untyped because production alone does not establish a partner fitness benefit (#749).

Participating Taxa: Clostridium acetobutylicum, Clostridium ljungdahlii

Metabolites: isopropanol (CHEBI:17824 · MediaIngredientMech · CMMMech), 2,3-butanediol (CHEBI:62064 · MediaIngredientMech · CMMMech)

Evidence

  • PMID:30391511 - SUPPORT (IN_VITRO)
    "resulted in the production of non-native metabolites, namely isopropanol"
  • PMID:30391511 - PARTIAL (IN_VITRO)
    "direct cell-to-cell interactions and material exchange among the two microbes"
  • PMID:32873766 - SUPPORT (IN_VITRO)
    "which C. ljungdahlii can in principle produce alone, but did not in control cultures"

Associated Datasets

Dataset Type Repository Accession
RNA-seq reads for the coculture, transwell, and monoculture arms
54 BioSamples (SAMN44010615-SAMN44010668) covering the Type I bottle comparison and the Type II transwell comparison, in biological triplicate. 		METATRANSCRIPTOMICS NCBI_BIOPROJECT PRJNA1167669

Knowledge gaps & discussions (2)

KNOWLEDGE_GAP OPEN Which partner-resolved fluxes and perturbations establish amino-acid transfer and hydrogenase-mediated benefit?

PMID:40298437 measures supernatant amino acids, recipient monoculture supplementation and early glucose consumption. These results support the proposed mechanisms without tracing donor-derived amino acids, ATP or local hydrogen flux, directly assaying hydrogenase feedback, or measuring species-specific reciprocal growth. Direct transfer and mediator perturbations would distinguish these routes from other contact or medium effects.

Attaches to: ecological_interactions#Gas syntrophy - CO2 and H2 transfer to the acetogen, ecological_interactions#Arginine cross-feeding to the acetogen, ecological_interactions#Histidine degradation feeding the acetogen, ecological_interactions#Proposed hydrogenase feedback relief through hydrogen removal, ecological_interactions#Contact-associated transcriptional response and proposed growth stimulation, ecological_interactions#Proposed amino-acid competition and product inhibition

KNOWLEDGE_GAP OPEN Which macromolecules transfer in the unmodified pair, and is fusion necessary for its product phenotype?

PMID:32873766 demonstrates wild-type structural fusion and describes protein-dye exchange, but its RNA assay uses C. acetobutylicum-Halo. PMID:38214507 demonstrates DNA acquisition and integration using a plasmid-bearing C. ljungdahlii donor and selected recipients, not the wild-type pairing; its node and arrow were removed from this graph with provenance retained in the review ledger. A separately scoped engineered record and exact-system transfer evidence would preserve these distinctions. Contact separation is not a fusion-specific intervention. The founding PMID:30391511 full body and the supplementary images were not inspected.

Attaches to: ecological_interactions#Interspecies cell fusion and cytoplasmic material exchange, ecological_interactions#Coculture isopropanol and 2,3-butanediol production

External Resources

Name Repository Resource ID
Seed publication - coculture transcriptional program
Open-access mSystems study of the coculture transcriptome, the amino-acid exchange, and the mutualism reclassification. 		OTHER PMID:40298437
  • PMID:40298437 - SUPPORT (IN_VITRO)
    "we used RNA sequencing to identify genes differentially expressed in this coculture using two types of comparisons"
Founding syntrophy publication
The 2019 Metabolic Engineering paper that built the coculture and reported the non-native metabolites. 		OTHER PMID:30391511
  • PMID:30391511 - SUPPORT (IN_VITRO)
    "consisting of the solventogen Clostridium acetobutylicum, which converts simple"
Cell-fusion structural evidence
The 2020 mBio paper with the electron microscopy and tomography that demonstrated the fusion. 		OTHER PMID:32873766
  • PMID:32873766 - SUPPORT (IN_VITRO)
    "transmission electron microscopy and electron tomography demonstrated cell wall and membrane fusions between the two organisms"
Interspecies DNA transfer
The 2024 mBio paper reporting plasmid DNA transfer and genomic integration. 		OTHER PMID:38214507
  • PMID:38214507 - SUPPORT (IN_VITRO)
    "we isolated C. acetobutylicum cells which acquired and integrated into their genome portions of plasmid DNA from a plasmid-carrying C. ljungdahlii strain"

Environmental Factors

Factor Value Unit
Chamber atmosphere 85% N2, 10% CO2, and 5% H2 N/A
  • PMID:40298437 - SUPPORT (IN_VITRO)
    "inside an anaerobic chamber (atmosphere composed of 85% N2, 10% CO2, and 5% H2)"
Headspace venting screw caps loosened N/A
  • PMID:40298437 - SUPPORT (IN_VITRO)
    "The screw cap bottle lids were loosened to allow accumulated gas to escape"
Physical separation control 0.4 µm permeable membrane N/A
  • PMID:40298437 - SUPPORT (IN_VITRO)
    "separated by a permeable membrane (0.4 µm pore size)"

Growth Media

Turbo CGM complex growth medium

Temperature 37.0 °C
Atmosphere ANAEROBIC

Composition

Component Concentration Unit CHEBI
yeast extract · MediaIngredientMech 5 g/L N/A

Preparation notes: A complex medium chosen because it supports both species; the paper cites its earlier work for the formulation rather than restating the full recipe, so only the yeast-extract concentration is asserted here. Pre-cultures were heat shocked at 80°C to kill non-sporulated cells before inoculation. Note that C. ljungdahlii does not use glucose in this system; the paper tracks its fructose consumption.

Evidence

PMID:40298437

"using the complex (5 g/L yeast extract) Turbo CGM growth medium"

PMID:40298437

"heat shocked at 80°C to kill non-sporulated cells"

Cross-Mech Suite Links

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HabitatMech: static anaerobic laboratory coculture in loosened screw-cap bottles ↗ TaxonMech: Clostridium acetobutylicum ↗ TraitMech: Clostridium acetobutylicum ↗ TaxonMech: Clostridium ljungdahlii ↗ TraitMech: Clostridium ljungdahlii ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗