Model Lignocellulose Formaldehyde Cross-Feeding Community

Community ID CommunityMech:000178

Ecological State ENGINEERED

Environment defined model lignocellulose laboratory culture
ENVO:01001405

A synthetic model lignocellulose-degrading community developed to study plant-biomass transformation and mitigation of toxic formaldehyde produced during breakdown of methoxylated aromatic compounds. The system includes Pseudomonas putida as a lignin degrader, Cellulomonas fimi as a cellulose degrader, Methylorubrum extorquens as a methylotrophic formaldehyde consumer, and Yarrowia lipolytica as an oleaginous yeast included in some consortium variants.

Taxonomy

Taxon	Ontology ID	Functional Roles	Abundance
Pseudomonas putida	NCBITaxon:303	PRIMARY_DEGRADER	ABUNDANT
doi:10.3390/microorganisms9020321 - SUPPORT (IN_VITRO) "Pseudomonas putida, a lignin degrader"
Cellulomonas fimi	NCBITaxon:1708	PRIMARY_DEGRADER	ABUNDANT
doi:10.3390/microorganisms9020321 - SUPPORT (IN_VITRO) "Cellulomonas fimi, a cellulose degrader" doi:10.3390/microorganisms9020321 - SUPPORT (IN_VITRO) "exceed the minimum inhibitory concentration for C. fimi"
Methylorubrum extorquens	NCBITaxon:408	CROSS_FEEDER	ABUNDANT
doi:10.3390/microorganisms9020321 - SUPPORT (IN_VITRO) "Methylorubrum extorquens, a methylotroph capable of using formaldehyde for growth"
Yarrowia lipolytica	NCBITaxon:4952	CROSS_FEEDER	COMMON
doi:10.3390/microorganisms9020321 - SUPPORT (IN_VITRO) "sometimes Yarrowia lipolytica, an oleaginous yeast"

Ecological Interactions

Taxon

Cross-feeding

Mutualism

Syntrophy

Competition

Commensalism

Niche partitioning

Colonization facilitation

Strain competition

Predation

Formaldehyde Toxicity from Aromatic Breakdown

COMPETITION

Source Taxon: Pseudomonas putida

Target Taxon: Cellulomonas fimi

Metabolites: formaldehyde (CHEBI:16842)

Biological Processes:

interspecies interaction between organisms (GO:0044419)

Evidence

doi:10.3390/microorganisms9020321 - SUPPORT (IN_VITRO)

"formaldehyde produced by P. putida growing on vanillic acid"
doi:10.3390/microorganisms9020321 - SUPPORT (IN_VITRO)

"exceed the minimum inhibitory concentration for C. fimi"

Methylotrophic Formaldehyde Mitigation

COMMENSALISM

Source Taxon: Methylorubrum extorquens

Target Taxon: Cellulomonas fimi

Metabolites: formaldehyde (CHEBI:16842)

Biological Processes:

metabolic process (GO:0008152)

Evidence

doi:10.3390/microorganisms9020321 - SUPPORT (IN_VITRO)

"presence of M. extorquens lowers those concentrations"

C. fimi and M. extorquens Metabolite Exchange

MUTUALISM

Source Taxon: Cellulomonas fimi

Target Taxon: Methylorubrum extorquens

Biological Processes:

interspecies interaction between organisms (GO:0044419)

Evidence

doi:10.3390/microorganisms9020321 - SUPPORT (IN_VITRO)

"mutualistic interaction between C. fimi and M. extorquens through metabolite exchange"

Resource Competition in Model Lignocellulose Medium

COMPETITION

Source Taxon: model lignocellulose consortium members

Target Taxon: model lignocellulose consortium members

Biological Processes:

interspecies interaction between organisms (GO:0044419)

Evidence

doi:10.3390/microorganisms9020321 - SUPPORT (IN_VITRO)

"resource competition"

External Resources

Name	Repository	Resource ID
Exact-system publication - Model Lignocellulose formaldehyde cross-feeding Primary publication describing the synthetic model lignocellulose consortium, formaldehyde production by P. putida, mitigation by M. extorquens, and metabolite exchange involving C. fimi.	OTHER	doi:10.3390/microorganisms9020321
doi:10.3390/microorganisms9020321 - SUPPORT (IN_VITRO) "model microbial consortium for studying lignocellulose degradation"

Environmental Factors

Factor	Value	Unit
Lignocellulose-relevant polymer recalcitrance	complex organic polymers such as lignocellulose	N/A
doi:10.3390/microorganisms9020321 - SUPPORT (IN_VITRO) "lignocellulose is one of the major obstacles to sustainable energy production from plant biomass"
Methoxylated aromatic-compound breakdown	formaldehyde generated from aromatic-substrate metabolism	N/A
doi:10.3390/microorganisms9020321 - SUPPORT (IN_VITRO) "breakdown of methoxylated aromatic compounds"
Toxin sensitivity differences	interspecies differences in toxin sensitivity	N/A
doi:10.3390/microorganisms9020321 - SUPPORT (IN_VITRO) "interspecies differences in growth requirements and toxin sensitivities"

Growth Media

Model Lignocellulose minimal growth medium

Atmosphere AEROBIC

Composition

Component	Concentration	Unit	CHEBI
cellobiose	N/A	N/A	CHEBI:17057
xylose	N/A	N/A	N/A
vanillic acid	N/A	N/A	N/A

Preparation notes: Defined minimal Model Lignocellulose medium used for reproducible coculture experiments; exact concentrations are not asserted in this record.

Evidence

doi:10.3390/microorganisms9020321

"defined minimal "Model Lignocellulose" growth medium"