Electrogen · Bidirectional EET · Iron reducer
Shewanella oneidensis MR-1
Also known as Alteromonas putrefaciens MR-1
Pseudomonadota · Gammaproteobacteria · Shewanellaceae
- Model organism
- Facultative
- Metabolically versatile
- Tier 1
01 · Identity
Identity
Where this organism sits in the tree of life, how to obtain it, and what a cell looks like.
Lineage
- domainBacteria
- ›phylumPseudomonadota
- ›classGammaproteobacteria
- ›orderAlteromonadales
- ›familyShewanellaceae
- ›genusShewanella
- ›speciesShewanella oneidensis MR-1
Culture collections & accessions
- ATCC
- ATCC 700550
- NCBI taxon
- 211586
- Genome
- GCF_000146165.2
- Status
- Type strain
Isolation
From Lake Oneida sediment, New York, USA by Myers CR, Nealson KH (1988).
Myers CR, Nealson KH (1988). Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor.
Genome
| Name | Sizekb | Accession | Replicon type |
|---|---|---|---|
| pMR-1 | 161.6 | AE014300.2 | Megaplasmid |
Cell morphology
Rod, Gram-negative (diderm)
length 2.5 (2–3) µm · width 0.5 (0.4–0.7) µm
- Motile: yes
- Pili: yes
- S-layer: no
- Outer-membrane vesicles: yes
- Spore-forming: no
02 · Electron transfer
Electron transfer
How electrons cross the cell envelope — the property that makes a microbe useful in an electrochemical system.
Mechanisms
- Outer-membrane cytochromes: yes
- Conductive pili / nanowires: yes
- Endogenous shuttles: yes
- Exogenous shuttles: yes
Nanowire conductivity 0.001 (0.0001–0.01) S/cm
Outer-membrane extension nanowires; lower conductivity than Geobacter cytochrome filaments. See Pirbadian 2014.
Redox ladder
- 1FMN -0.219 V · endogenous
- 2riboflavin -0.208 V · endogenous
- 3CymA -0.19 V · Inner membrane · 4 hemes
- 4MtrA -0.14 V · Periplasm · 10 hemes
- 5OmcA -0.12 V · Outer membrane · 10 hemes
- 6MtrC -0.1 V · Outer membrane · 10 hemes
Cytochromes (6)
| Name | Location | Hemes | E°′V | Structure |
|---|---|---|---|---|
| CymA | Inner membrane | 4 | -0.19 | — Quinone-pool-coupled tetraheme; entry point for MtrCAB pathway. |
| MtrA | Periplasm | 10 | -0.14 | PDB 6R2Q Periplasmic decaheme of the MtrCAB porin-cytochrome complex. |
| MtrB | Outer membrane | — | — | PDB 6R2Q β-barrel porin component of MtrCAB; not a cytochrome itself but harbors MtrA. |
| MtrC | Outer membrane | 10 | -0.1 | PDB 4LM8 Outer-membrane decaheme; primary electron transfer to electrode/Fe(III). |
| OmcA | Outer membrane | 10 | -0.12 | PDB 4LMH Outer-membrane decaheme; binds Fe(III) and electrode surface. |
| STC | Periplasm | 4 | — | — Small tetraheme cytochrome; cytoplasmic-pool-to-MtrA shuttle. |
Electron shuttles (2)
- FMN · endogenous · E°′ -0.219 V · 0.05 µM/OD600
Co-secreted with riboflavin; functions analogously.
- riboflavin · endogenous · E°′ -0.208 V · 0.13 µM/OD600
Released into the medium during growth; binds MtrC/OmcA to facilitate single-step electron transfer.
Direct transfer — detail
- Completeness
- Mapped
Mediated transfer — detail
- Completeness
- Mapped
03 · Growth envelope
Growth envelope
The conditions this organism tolerates and what it eats and breathes — the operating window for a reactor.
Energy metabolism
Electron donors
- Lactate
- Formate
- H2
Electron acceptors
- O2
- Fe(III)
- Mn(IV)
- Nitrate
- Fumarate
- Dmso
- Tmao
- Anode
- S2O3
- U(VI)
Carbon sources
- Lactate
- Pyruvate
- Formate
- N-acetylglucosamine
- amino acids
- Respiratory: yes
- Fermentative: no
Metabolism — detail
- ATP synthase type
- Proton dependent
- Energy conservation mechanism
- Oxidative phosphorylation
Growth kinetics
From 2 DB row(s) across 1 paper(s); source units: h⁻¹. Pooled across substrates: glucose, lactate — substrate-specific breakdown in per_substrate. Includes engineered/variant strings: Shewanella oneidensis MR-1(pBBR-glk-galP). Full provenance: services/ml-engine/data/kinetics-extracted/per-strain-aggregated.json.
From 1 DB row(s) across 1 paper(s); source units: mg/L. Full provenance: services/ml-engine/data/kinetics-extracted/per-strain-aggregated.json.
| Substrate | µ max | Observations |
|---|---|---|
| Glucose | 0.014 h⁻¹ | 1 |
| Lactate | 0.35 h⁻¹ | 1 |
04 · Growth & electron-transfer kinetics
Growth & electron-transfer kinetics
How fast this organism grows and how hard it pushes electrons into an anode, as the corpus reports it, and what those constants imply when you run them.
Kinetic evidence
| Parameter | Median | 10–90 % | n | Source |
|---|---|---|---|---|
| Max. specific growth rate μmax | 0.014 h⁻¹ | — | 1 | 1 paper |
| Half-saturation constant Ks | 124 mg/L | — | 1 | 1 paper |
| Biomass yield Y | 0.1 g/g | 0.05–0.18 | 3 | genus prior · 3 refs |
| Decay coefficient kd | Not in the corpus yet | |||
| Exchange current density i₀ | Not in the corpus yet | |||
| Transfer coefficient α | Not in the corpus yet | |||
| Tafel slope | Not in the corpus yet | |||
Median of the extracted values, the 10–90 % spread behind it and how many values it pools.
1 rows were not pooled: their unit could not be converted unambiguously.
Evidence rows (3)
- Max. specific growth rate μmax0.014 h⁻¹Not verifiedspecies rowconfidence 1
Metabolic Characteristics of a Glucose-Utilizing Shewanella oneidensis Strain Grown under Electrode-Respiring Conditions · 2015 · 10.1371/journal.pone.0138813
“This difference in the current densities may reflect a difference in the growth rates of this strain in GMM and LMM (0.014 h⁻¹ and 0.35 h⁻¹, respectively, under fumarate-reducing conditions).”
- Half-saturation constant Ks124 mg/LNot verifiedspecies rowconfidence 1
Performance of a Batch Operation Microbial Fuel Cell (MFC) with Cobalt Micronutrient Addition Based on Kinetic Models · 2024 · 10.9767/bcrec.20259
“Utami reported that MFCs with tempeh waste substrate produced a kinetic parameter value Ks of 124 mg/L with a power density of 0.033 mW/m² [10].”
Listed, not pooled (1)
- Max. specific growth rate μmax0.35 h⁻¹Not verifiedspecies rowconfidence 1
Metabolic Characteristics of a Glucose-Utilizing Shewanella oneidensis Strain Grown under Electrode-Respiring Conditions · 2015 · 10.1371/journal.pone.0138813
“This difference in the current densities may reflect a difference in the growth rates of this strain in GMM and LMM (0.014 h⁻¹ and 0.35 h⁻¹, respectively, under fumarate-reducing conditions).”
Not used in an estimate · substrate: lactate; the pooled substrate is glucose
Genus-level prior: Shewanella oneidensis
A genus-level prior is a summary for the whole genus, not a measurement on this strain.
Constants that drive the simulation
Scenario — values you set, not evidence
Not enough evidence to simulate
No Biomass yield Y for this organism in the corpus yet.
- Biomass yield Y
2 linked papers report kinetic constants for it; extraction is pending. See its papers
Driving force per redox carrier
- 1FMN -0.219 V · endogenous
- 2riboflavin -0.208 V · endogenous
- 3CymA -0.19 V · Inner membrane · 4 hemes
- 4MtrA -0.14 V · Periplasm · 10 hemes
- 5OmcA -0.12 V · Outer membrane · 10 hemes
- 6MtrC -0.1 V · Outer membrane · 10 hemes
E_anode − E_m at an anode potential of 0 V vs SHE.
- FMN+219 mV · downhill
- riboflavin+208 mV · downhill
- CymA+190 mV · downhill
- MtrA+140 mV · downhill
- OmcA+120 mV · downhill
- MtrC+100 mV · downhill
These curves are a Monod and Nernst-Monod idealisation (after Marcus et al. 2007 and Torres et al. 2008), parameterised only by the constants listed above: each one carries its n and its 10–90 % range, and a constant with n = 1 has no spread at all. No diffusion inside the biofilm, no detachment, no coulombic-efficiency split. The scenario values are yours, not evidence.
05 · Performance
Performance
Reported electrochemical output, the role it plays in a reactor, and what it produces.
Role in a reactor
06 · Ecology & biofilm
Ecology & biofilm
How it lives on an electrode, who it partners with, and where it is found in nature.
Biofilm
- Forms biofilm: yes
Preferred electrode materials
- carbon cloth
- graphite felt
- ITO
- Gold
Ecosystems
- Freshwater
- Sediment freshwater
Isolation sources
- sediment, Lake Oneida, New York, USA
07 · Applications, engineering & safety
Applications, engineering & safety
Where it has been put to work, how tractable it is to engineer, and what handling it requires.
Applications (4)
- BiosensorTRL 5/9
- Bioelectricity generationTRL 4/9
- Bioremediation metalsTRL 4/9
- Research model organism
Engineering
Reactor compatibility
- MFC single chamber
- MFC dual chamber
- MEC
Engineering history (2)
- 1988 Wild type isolation
Type strain isolated as MR-1 (Manganese Reducer 1).
1988 · Myers CR, Nealson KH 1988DOI
- 2009 Engineered
ΔmtrC/ΔomcA double knockout — abolishes Fe(III)/anode reduction.
2010 · Bretschger O, et al. (2007); Coursolle D, et al. (2010).
Genetics
- Genetically tractable: yes
Key EET genes
- mtrA
- mtrB
- mtrC
- mtrD
- mtrE
- mtrF
- omcA
- cymA
qPCR targets
- mtrB
- mtrC
- omcA
- cymA
Transformation methods
- Electroporation
- Conjugation
Vectors
- pBBR1MCS-derived suicide vectors
- pSMV3
CRISPR systems
- CRISPRi-dCas9 (heterologous)
Reporter genes
- GFP
- lacZ
Inducible promoters
- arabinose pBAD
- rhamnose pRha
Transposon libraries
- EZ-Tn5 in MR-1 (Bouhenni 2005)
Genome annotation: expert curated.
Omics studies (2)
Biosafety
- Pathogen: no
Modeling assets
- Genome-scale metabolic model: yes
- Kinetic model: yes
- iSO783
Linked GEM: iSO783
08 · Sources & data quality
Sources & data quality
Every value above traces to a citation. This is how complete and how confident the record is.
Record quality
Literature reviewed 2026-04-26 · schema v1.2.0 · updated 2026-05-14 · imported 2026-04-28
Per-field confidence
- Genome metadata.size (bp)
- High
- EET mechanism.mediated transfer.shuttles
- High
- EET mechanism.direct transfer.cytochromes
- High
References (3)
- Myers CR, Nealson KH (1988). Bacterial manganese reduction. Science 240:1319-1321.
- Marsili E, et al. (2008). Shewanella secretes flavins. PNAS 105:3968-3973.doi:10.1073/pnas.0710525105
- Pirbadian S, et al. (2014). Shewanella oneidensis nanowires are OM/periplasmic extensions. PNAS 111:12883-12888.doi:10.1073/pnas.1410551111
Version history
- 2026-04-27 · v1.2.0 · messai_curation
- Added MtrCAB cytochrome inventory with PDB IDs and midpoint potentials.
- Added structured riboflavin/FMN shuttles with redox potentials.
- Added genome_metadata with megaplasmid pMR-1.
- Added genetic_tools structured catalog.