Prymnesium parvum B12-Limited SynCom

Community ID CommunityMech:000381

Ecological State ENGINEERED

Environment laboratory marine algal-bacterial SynCom — ontology label: laboratory environment
ENVO:01001405 · HabitatMech ↗

Modeled Environment marine environment
ENVO:01000320 · HabitatMech ↗

A defined 16-member marine algal-bacterial holobiont in which Prymnesium parvum CCAP 646/6 was cocultured in L1 medium with a 15-strain synthetic bacterial community and monitored under nitrogen, phosphorus, or vitamin B12 limitation. Patron et al. (2026) inoculated all SynCom bacteria in equal proportions and compared photobioreactor cultures with and without the SynCom for 14 days. Nitrogen and phosphorus limitation did not reveal a major growth benefit from the SynCom, whereas B12 limitation triggered a mutualistic state in which bacterial cobalamin provisioning rescued algal growth, B12-producing bacteria upregulated cobalamin biosynthesis, and B12-auxotrophic bacteria induced vitamin transport and B12-dependent enzymes.

Taxonomy

Taxon	Ontology ID	Functional Roles	Abundance
Prymnesium parvum CCAP 646/6 — ontology label: Prymnesium parvum	NCBITaxon:97485 · TaxonMech · TraitMech	PRIMARY_PRODUCER CROSS_FEEDER	COMMON
PMID:42549325 - SUPPORT (IN_VITRO) "P. parvum (CCAP 646/6) was acclimated for two weeks in L1 medium"
Cyclobacterium sp. 09-022 — ontology label: Cyclobacterium	NCBITaxon:68288 · TaxonMech · TraitMech	CROSS_FEEDER	COMMON
PMID:42549325 - SUPPORT (IN_VITRO) "09-022 Cyclobacterium sp. "
Maribacter sp. 09-009 — ontology label: Maribacter	NCBITaxon:252356 · TaxonMech · TraitMech	CROSS_FEEDER	COMMON
PMID:42549325 - SUPPORT (IN_VITRO) "09-009 Maribacter sp. "
Muricauda sp. 10-244 — ontology label: Allomuricauda	NCBITaxon:111500 · TaxonMech · TraitMech	CROSS_FEEDER	COMMON
PMID:42549325 - SUPPORT (IN_VITRO) "10-244 Muricauda sp. "
Marinovum algicola 19-037 — ontology label: Marinovum algicola	NCBITaxon:42444 · TaxonMech · TraitMech	CROSS_FEEDER	COMMON
PMID:42549325 - SUPPORT (IN_VITRO) "19-037 Marinovum algicola B12 producer "
Marivita cryptomonadis 10-255 — ontology label: Marivita cryptomonadis	NCBITaxon:505252 · TaxonMech · TraitMech	CROSS_FEEDER	COMMON
PMID:42549325 - SUPPORT (IN_VITRO) "10-255 Marivita cryptomonadis "
Roseobacter sp. 09-029 — ontology label: Roseobacter	NCBITaxon:2433 · TaxonMech · TraitMech	CROSS_FEEDER	COMMON
PMID:42549325 - SUPPORT (IN_VITRO) "09-029 Roseobacter sp. B12 producer "
Thalassospira sp. 19-025 — ontology label: Thalassospira	NCBITaxon:168934 · TaxonMech · TraitMech	CROSS_FEEDER	COMMON
PMID:42549325 - SUPPORT (IN_VITRO) "19-025 Thalassospira sp. B12 producer "
Alteromonas sp. 002 19-002 — ontology label: Alteromonas	NCBITaxon:226 · TaxonMech · TraitMech	CROSS_FEEDER	COMMON
PMID:42549325 - SUPPORT (IN_VITRO) "19-002 Alteromonas sp. 002 "
Alteromonas sp. 005 19-005 — ontology label: Alteromonas	NCBITaxon:226 · TaxonMech · TraitMech	CROSS_FEEDER	COMMON
PMID:42549325 - SUPPORT (IN_VITRO) "19-005 Alteromonas sp. 005 "
Halomonas alkaliphila 09-027 — ontology label: Vreelandella alkaliphila	NCBITaxon:272774 · TaxonMech · TraitMech	CROSS_FEEDER	COMMON
PMID:42549325 - SUPPORT (IN_VITRO) "09-027 Halomonas alkaliphila B12 producer "
Halomonas sp. 19-001 — ontology label: Halomonas	NCBITaxon:2745 · TaxonMech · TraitMech	CROSS_FEEDER	COMMON
PMID:42549325 - SUPPORT (IN_VITRO) "19-001 Halomonas sp. B12 producer "
Marinobacter sp. 10-113 — ontology label: Marinobacter	NCBITaxon:2742 · TaxonMech · TraitMech	CROSS_FEEDER	COMMON
PMID:42549325 - SUPPORT (IN_VITRO) "10-113 Marinobacter sp. "
Vibrio aestuarianus 23-001 — ontology label: Vibrio aestuarianus	NCBITaxon:28171 · TaxonMech · TraitMech	CROSS_FEEDER	COMMON
PMID:42549325 - SUPPORT (IN_VITRO) "23-001 Vibrio aestuarianus "
Vibrio diazotrophicus 23-002 — ontology label: Vibrio diazotrophicus	NCBITaxon:685 · TaxonMech · TraitMech	CROSS_FEEDER	COMMON
PMID:42549325 - SUPPORT (IN_VITRO) "23-002 Vibrio diazotrophicus Diazotroph "
Pseudomonas stutzeri 23-003 — ontology label: Stutzerimonas stutzeri	NCBITaxon:316 · TaxonMech · TraitMech	CROSS_FEEDER	COMMON
PMID:42549325 - SUPPORT (IN_VITRO) "23-003 Pseudomonas stutzeri Diazotroph "

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.

Taxon

Other

B12-limited holobiont mutualism

The study reports a whole-community algal benefit and increased bacterial abundance in the relevant nutrient-limited comparison. PARTIAL: these positive observations support the authors mutualism interpretation but do not identify a strain-resolved transfer route, establish each partners causal contribution or show that the composite outcome causes biosynthetic transcription.

Metabolites: vitamin B12 (CHEBI:176843 · MediaIngredientMech · CMMMech)

Biological Processes:

biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)

Evidence

PMID:42549325 - SUPPORT (IN_VITRO)

"B12-limitation triggered a strong mutualistic interaction in which the SynCom enabled a three-fold increase in algal biomass "
PMID:42549325 - SUPPORT (IN_VITRO)

"bacterial B12 production alleviated the limitation "

Cobalamin biosynthesis by B12-producing SynCom members

The study reports community enrichment and cobalamin-biosynthesis transcription. PARTIAL: transcription is not measured secretion or transfer flux. The abstract/discussion and focused results disagree on one producer identity; the disputed graph participant is omitted pending source reconciliation, without substituting another strain.

Participating Taxa: Marinovum algicola 19-037, Roseobacter sp. 09-029

Metabolites: cobalamin (CHEBI:30411 · MediaIngredientMech · CMMMech)

Biological Processes:

cobalamin biosynthetic process (GO:0009236 · PathwayMech)

Evidence

PMID:42549325 - SUPPORT (IN_VITRO)

"B12-producers (Marinovum algicola, Roseobacter sp., Halomonas sp.) upregulated cobalamin biosynthesis exclusively under B12-limitation "
PMID:42549325 - SUPPORT (IN_VITRO)

"Enrichment of B12-producing taxa (i.e. Marinovum algicola, Roseobacter sp., Halomonas sp.) under B12-lim coincided with the upregulation of cobalamin biosynthesis pathways "

Auxotrophic SynCom B12 acquisition

Non-producing members induced cobalamin transporters and B12-dependent functions. PARTIAL: these measured transcript responses support the authors acquisition interpretation, but do not directly quantify vitamin flux or demonstrate a competitive fitness cost.

Participating Taxa: Cyclobacterium sp. 09-022, Marivita cryptomonadis 10-255, Marinobacter sp. 10-113, Pseudomonas stutzeri 23-003

Metabolites: cobalamin (CHEBI:30411 · MediaIngredientMech · CMMMech)

Biological Processes:

biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)

Evidence

PMID:42549325 - SUPPORT (IN_VITRO)

"several B12-auxotrophic taxa induced B12-transport and B12-requiring enzymes, indicating active vitamin exchange within the holobiont "
PMID:42549325 - SUPPORT (IN_VITRO)

"non-B12 producers Cyclobacterium qasimii, Marivita cryptomonadis, Marinobacter sp., and Pseudomonas stutzeri, which also upregulated B12-dependent genes, strongly induced most of their B12 transporters under B12-lim conditions "

Algal organic-matter support of heterotrophic bacteria

HYPOTHESIZED: the authors propose that algal organic matter supports heterotrophic bacteria as part of reciprocal exchange. Retain this interpretation separately from measured community outcomes; the exact carbon-transfer and vitamin-release routes remain unresolved.

Participating Taxa: Prymnesium parvum CCAP 646/6

Biological Processes:

photosynthesis (GO:0015979 · PathwayMech)
biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)

Downstream Effects:

→ B12-limited holobiont mutualism

HYPOTHESIZED: algal organic-matter support could contribute to the reported reciprocal community benefit. This existing direction expresses the authors interpretation, not a directly traced carbon flux or proof of each partners contribution.

Evidence

PMID:42549325 - SUPPORT (IN_VITRO)

"Heterotrophic bacteria dependent on algal organic matter synthesize and mobilize B12 under nutrient stress, and both partners utilize it. "

Associated Datasets

Dataset	Type	Repository	Accession
P. parvum SynCom metabarcoding, RNA-seq, and bacterial genome sequencing European Nucleotide Archive project containing metabarcoding, RNA-seq, and bacterial genome sequencing data for the nutrient-limited P. parvum SynCom.	MULTI_OMICS	ENA	PRJEB106332
P. parvum SynCom metabolomics and prymnesin mass-spectrometry data Full-scan and MS/MS metabolomics data for intracellular and extracellular extracts from the nutrient-limited P. parvum SynCom experiment.	METABOLOMICS	OTHER
Prymnesium parvum genome assembly used for RNA-seq mapping P. parvum genome assembly used for host transcriptome mapping.	GENOMICS	OTHER

Knowledge gaps & discussions (2)

KNOWLEDGE_GAP OPEN Does P. parvum acquire bacterial B12 primarily from passive extracellular release, bacterial lysis, prophage- or phage-mediated release, or bacterivory of the SynCom partners?

The source supports bacterial B12 production and auxotrophic acquisition but explicitly leaves the cellular route of vitamin release and transfer unresolved.

Attaches to: ecological_interactions#B12-limited holobiont mutualism, ecological_interactions#Cobalamin biosynthesis by B12-producing SynCom members

1 proposed experiment(s)

Test B12 exporter and lysis routes in producing strains
Approach: defined-coculture growth assay with targeted bacterial genetics
Decision: Loss of algal rescue in a specific mutant background, restored by exogenous B12, would prioritize that release route.

1 evidence item(s)

full_text SUPPORT PMID:42549325

The precise mechanism of B12 transfer remains unresolved. Not only are the potential acquisition routes unclear, but the identity of bacterial exporters mediating vitamin release is also unknown.

States the open mechanistic question around B12 export and acquisition.

KNOWLEDGE_GAP OPEN Which source-supported observations can be distinguished from inferred exchange?

Two outcome-to-transcription arrows were removed because correspondence does not establish the encoded causal direction. Positive whole-community outcomes and expression findings remain; no reverse arrows or new biological mechanisms were added. The source reports no detected extracellular B12 and leaves transfer unresolved. Producer attribution conflicts between sections and remains #1728. Existing non-graph roles and proposed experiments are not certified by this review; no new experimental designs or growth-optimization details were added.

Attaches to: ecological_interactions#B12-limited holobiont mutualism, ecological_interactions#Cobalamin biosynthesis by B12-producing SynCom members, ecological_interactions#Auxotrophic SynCom B12 acquisition, ecological_interactions#Algal organic-matter support of heterotrophic bacteria

2 evidence item(s)

IN_VITRO SUPPORT PMID:42549325

The precise mechanism of B12 transfer remains unresolved. Not only are the potential acquisition routes unclear, but the identity of bacterial exporters mediating vitamin release is also unknown.

States the open mechanistic question around B12 export and acquisition.

IN_VITRO SUPPORT PMID:42549325

several B12-auxotrophic taxa induced B12-transport and B12-requiring enzymes, indicating active vitamin exchange within the holobiont

Supports transcript induction and the authors exchange interpretation, not directly measured transfer or competition.

Environmental Factors

Factor	Value	Unit
vitamin B12 limitation	7.4 x 10^-6 uM vitamin B12	N/A
PMID:42549325 - SUPPORT (IN_VITRO) "vitamin B12-limited (B12-lim; B12 adjusted to 7.4 × 10−6 μM) conditions "
nitrogen limitation	62 uM N	N/A
PMID:42549325 - SUPPORT (IN_VITRO) "N- (N-lim; N adjusted to 62 μM), P- (P-lim; P adjusted to 2.2 μM) "
phosphorus limitation	2.2 uM P	N/A
PMID:42549325 - SUPPORT (IN_VITRO) "P- (P-lim; P adjusted to 2.2 μM)"
oxic continuous-light phenotyping	100 umol photons m-2 s-1 at pH 8.2 and 20 C	N/A
PMID:42549325 - SUPPORT (IN_VITRO) "Cultures were grown in photobioreactors under continuous light (100 μmol photons m−2 s−1), at 20°C, and pH 8.2 " PMID:42549325 - SUPPORT (IN_VITRO) "the oxygen sensitivity of the nitrogenase complex may have constrained activity in our oxic batch cultures "

Growth Media

nutrient-limited L1 marine algal medium

pH 8.2

Temperature 20 C

Atmosphere AEROBIC

Composition

Component	Concentration	Unit	CHEBI
L1 medium · MediaIngredientMech	N/A	N/A	N/A
vitamin B12 · MediaIngredientMech	7.4 x 10^-6	uM in B12-limited treatment	CHEBI:176843
dissolved nitrogen · MediaIngredientMech	62	uM N in N-limited treatment	N/A
dissolved phosphorus · MediaIngredientMech	2.2	uM P in P-limited treatment	N/A

Preparation notes: P. parvum was acclimated to N-, P-, or B12-limited L1 medium for two weeks before the 15-strain bacterial SynCom was added to the coculture treatments.

Evidence

PMID:42549325

"P. parvum (CCAP 646/6) was acclimated for two weeks in L1 medium "

PMID:42549325

"In co-cultures treatments, the defined SynCom was added at a total density of 1 × 105 cells ml−1. "

Cross-Mech Suite Links

Explore related entities across the CultureBotAI X-Mech knowledge bases:

HabitatMech: laboratory marine algal-bacterial SynCom ↗ TaxonMech: Prymnesium parvum CCAP 646/6 ↗ TraitMech: Prymnesium parvum CCAP 646/6 ↗ TaxonMech: Cyclobacterium sp. 09-022 ↗ TraitMech: Cyclobacterium sp. 09-022 ↗ TaxonMech: Maribacter sp. 09-009 ↗ TraitMech: Maribacter sp. 09-009 ↗ TaxonMech: Muricauda sp. 10-244 ↗ TraitMech: Muricauda sp. 10-244 ↗ TaxonMech: Marinovum algicola 19-037 ↗ TraitMech: Marinovum algicola 19-037 ↗ TaxonMech: Marivita cryptomonadis 10-255 ↗ TraitMech: Marivita cryptomonadis 10-255 ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗