A methane-consuming freshwater lake sediment community from Lake Washington, Seattle, represented by methane-fed sediment microcosms and follow-up community modeling studies. Methane addition selects both bona fide methane-oxidizing Methylococcaceae and non-methanotrophic methylotrophic Methylophilaceae, supporting a guild-based community rather than a single-organism methane oxidation model. Oxygen tension structures specific partnerships: Methylosarcina and Methylophilus dominate higher-oxygen microcosms, whereas Methylobacter and Methylotenera dominate lower-oxygen microcosms. The system is DOE-relevant because it links methane mitigation, freshwater sediment carbon cycling, methylotroph ecology, and genome-scale modeling of methane-cycling communities.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Lake Washington methane-consuming microbial community — ontology label: cellular organisms | NCBITaxon:131567 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
CROSS_FEEDER
|
N/A |
|
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| Methylococcaceae methanotrophs — ontology label: Methylococcaceae | NCBITaxon:403 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
|
DOMINANT |
|
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| Methylophilaceae non-methanotrophic methylotrophs — ontology label: Methylophilaceae | NCBITaxon:32011 · TaxonMech · TraitMech |
CROSS_FEEDER
|
DOMINANT |
|
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| Methylobacter | NCBITaxon:429 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
|
DOMINANT |
|
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| Methylotenera | NCBITaxon:359407 · TaxonMech · TraitMech |
CROSS_FEEDER
|
DOMINANT |
|
|||
| Methylomonas | NCBITaxon:416 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
|
N/A |
|
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| Methylosarcina — ontology label: Methylosarcina fibrata | NCBITaxon:105972 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
|
N/A |
|
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| Methylophilus | NCBITaxon:16 · TaxonMech · TraitMech |
CROSS_FEEDER
|
N/A |
|
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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.
Methanotroph-Methylotroph Guild Coupling
CROSS_FEEDINGMethane-fed sediment microcosms co-enrich Methylococcaceae and non-methanotrophic Methylophilaceae. PARTIAL - growth and prior stable-isotope studies support inferred methane-derived carbon coupling between guilds, but this experiment does not identify the transferred compound, directly trace methanol donation or establish reciprocal benefit. Family-level coupling is not a resolved strain pair or a universal partnership.
Source Taxon: Methylococcaceae methanotrophs
Target Taxon: Methylophilaceae non-methanotrophic methylotrophs
Metabolites: methane (CHEBI:16183 · MediaIngredientMech · CMMMech)
Biological Processes:
- methane metabolic process (GO:0015947 · PathwayMech)
Evidence
-
PMID:25755930 - PARTIAL (IN_VITRO)"likely involves communities composed of different functional guilds"
-
PMID:25755930 - PARTIAL (IN_VITRO)"rather than a single type of microbe"
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PMID:25755930 - PARTIAL (IN_VITRO)"we do not have information regarding how a methanotroph can provide carbon to a community of non-methanotrophs"
Oxygen-Regime Dependent Guild Composition
Under repeated methane feeding and daily gas resetting, initial oxygen regimes changed 16S relative guild composition after 10 and 16 weeks. Higher-oxygen treatments favored Methylosarcina/Methylophilus, whereas lower-oxygen treatments favored Methylobacter/Methylotenera, with intermediate mixtures and replicate exceptions. Low treatments became hypoxic before replenishment; these were not constant dissolved-oxygen levels. This establishes treatment-dependent composition, not a unique molecular partnership mechanism or absolute viable abundance. Listed participants are the reliable canonical aggregate/families/genera, not the incorrectly grounded Methylosarcina species.
Participating Taxa: Lake Washington methane-consuming microbial community, Methylococcaceae methanotrophs, Methylophilaceae non-methanotrophic methylotrophs, Methylobacter, Methylotenera, Methylophilus
Biological Processes:
- methane metabolic process (GO:0015947 · PathwayMech)
PARTIAL - changing the oxygen-feeding regime selects different relative abundances of methanotroph and methylotroph genera within the methane-fed guilds. This alters the observed guild composition, not a demonstrated specific carbon-transfer reaction or reciprocal benefit; the treatments also differ in time spent hypoxic.
Evidence
-
PMID:25755930 - SUPPORT (IN_VITRO)"different species persisted under different oxygen tensions"
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PMID:25755930 - SUPPORT (IN_VITRO)"oxygen availability is at least one major factor determining specific partnerships in methane oxidation"
Modeled Methylomonas-To-Methylobacter Formaldehyde Transfer
An OptCom genome-scale model of Methylomonas sp. LW13 and Methylobacter tundripaludum 21/22 reports conditional formaldehyde transfer from Methylomonas to Methylobacter. With imposed MB:ML growth ratios, uptake occurs in the synthetic 0.05:1 scenario but not the sediment 9.3:1 scenario. These ratios are constraints, not predicted abundances. PARTIAL - optimization, borrowed biomass/maintenance parameters and a formaldehyde-inhibition constraint shape this result; no transfer was experimentally validated here. Conflicting wording elsewhere in the source remains unresolved under #1554, so this is a qualified reported prediction, not verified flux.
Source Taxon: Methylomonas
Target Taxon: Methylobacter
Metabolites: methane (CHEBI:16183 · MediaIngredientMech · CMMMech), carbon dioxide (CHEBI:16526 · MediaIngredientMech · CMMMech), formaldehyde (CHEBI:16842 · MediaIngredientMech · CMMMech)
Biological Processes:
- methane metabolic process (GO:0015947 · PathwayMech)
Evidence
-
PMID:32655999 - PARTIAL (COMPUTATIONAL)"Methylobacter takes up some of the secreted formaldehyde from Methylomonas as a carbon source in addition to methane under the synthetic condition"
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PMID:32655999 - PARTIAL (COMPUTATIONAL)"the experimentally observed species abundance ratio was imposed on the growth rates"
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
|
Oxygen-gradient Lake Washington methane-consuming microcosms
PubMed-indexed PeerJ study of oxygen availability and community composition in methane-fed Lake Washington sediment microcosms. |
AMPLICON_16S | OTHER | PMID:25755930 |
|
Lake Washington methanotroph genome-scale community modeling
Genome-scale metabolic modeling study of Lake Washington Methylobacter and Methylomonas methane-cycling interactions. |
OTHER | OTHER | PMID:32655999 |
|
Lake Washington Methylophilaceae ecotype genomics
Cultivation and genome sequencing study of Lake Washington Methylophilaceae ecotypes relevant to methane oxidation-associated methylotroph communities. |
GENOMICS | OTHER | PMID:25058595 |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which compounds mediate guild coupling, and can the conditional two-methanotroph model result be reproduced?
Retain oxygen-regime selection of guild composition, but remove the cross-study arrow to the separate two-methanotroph model. The 2015 microcosms infer carbon coupling without identifying the mediator or reciprocal benefit; nitrogen-metabolism explanations are hypotheses. The 2020 model reports Methylomonas-to-Methylobacter formaldehyde transfer under imposed synthetic ratios, not the sediment ratio, and environmental CO2 export. Do not confuse the two methanotrophs with the methanotroph/methylotroph guild pair. Nutrient-rich dominance and formaldehyde-export statements conflict internally, tracked in #1554. Full main bodies were read, but no original figures, S4 workbook, SBML models or executable solutions were audited; the public supplemental endpoint failed HTTP500. #1553 tracks the Methylosarcina genus/species mismatch and other taxonomy/metadata. Omit that misgrounded species from explicit participants rather than silently validating it; the resulting connectivity warning is an unresolved roster defect, not grounds to invent an edge.
Attaches to: ecological_interactions#Methanotroph-Methylotroph Guild Coupling, ecological_interactions#Oxygen-Regime Dependent Guild Composition, ecological_interactions#Modeled Methylomonas-To-Methylobacter Formaldehyde Transfer
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Methane amendment | methane supplied at the same concentration in each microcosm | N/A |
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| Oxygen tension | five different oxygen tensions | N/A |
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| Methane-oxygen countergradient | freshwater lake methane-oxygen countergradient | N/A |
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Growth Media
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