Home ← Back to Communities Text Map Taxonomic UMAP Sequence Map Network Schema All Mech projects

South Bay Salt Pond Methane Restoration Microbial Community

Community ID CommunityMech:000246
Ecological State PERTURBED
Environment former industrial salt pond sediment — ontology label: sediment
ENVO:00002007 · HabitatMech ↗

Natural sediment microbial communities from former industrial salt ponds, a restored salt pond, and a reference tidal wetland in the San Francisco South Bay Ravenswood complex. DOE JGI-supported 16S rRNA amplicon and shotgun metagenomic analyses linked wetland restoration state to microbial composition, metabolic potential, and methane flux. Unrestored salt ponds had elevated methane emissions that were positively correlated with salinity and sulfate, while the restored pond resembled the reference wetland more closely and showed lower salinity, sulfate, and methane emissions. The study implicates archaeal methanogenesis and bacterial methylphosphonate degradation as methane-generating mechanisms in these coastal wetland sediments.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
South Bay salt pond sediment microbial communities — ontology label: cellular organisms NCBITaxon:131567 · TaxonMech · TraitMech
PRIMARY_DEGRADER SECONDARY_FERMENTER SYNTROPHIC_PARTNER
N/A
unrestored salt pond methane-linked bacteria — ontology label: Bacteria NCBITaxon:2 · TaxonMech · TraitMech
PRIMARY_DEGRADER
N/A
salt pond methanogenic archaea — ontology label: Archaea NCBITaxon:2157 · TaxonMech · TraitMech
SYNTROPHIC_PARTNER
COMMON

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 South Bay Salt Pond Methane Restoration Microbial Community Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
Taxon
Other

Restoration-State Community Composition Association

Community composition differed among the sampled unrestored ponds, restored pond and reference wetland, with restored and reference communities more similar to one another. This cross-site association is consistent with restoration-related environmental filtering but does not isolate restoration as a cause or demonstrate distinct niches that reduce competition.

Biological Processes:

Evidence

  • doi:10.1038/s41396-021-01067-w - SUPPORT (COMPUTATIONAL)
    "with restored/reference wetland communities more similar to each other than to those of unrestored salt ponds"

Archaeal Methanogenesis Evidence and Methane Flux Association

Archaeal methanogenesis-gene abundances correlated positively with methane flux across sites. A separate unrestored-pond microcosm comparison supported methane production from methylated substrates, while acetate did not significantly stimulate production. These findings support a methanogenic contribution, not a quantified in-situ pathway flux, attribution to every archaeon or syntrophic product-removal feedback.

Participating Taxa: salt pond methanogenic archaea

Metabolites: methane (CHEBI:16183 · MediaIngredientMech · CMMMech)

Biological Processes:

Evidence

  • doi:10.1038/s41396-021-01067-w - SUPPORT (COMPUTATIONAL)
    "Archaeal methanogenesis genes were positively correlated with methane flux"
  • doi:10.1038/s41396-021-01067-w - SUPPORT (IN_VITRO)
    "Acetate addition did not stimulate significant methane production, and control incubations also exhibited little change in methane production rates."
  • doi:10.1038/s41396-021-01067-w - SUPPORT (IN_VITRO)
    "the substrate addition experiment demonstrated the conversion of trimethylamine and methanol to methane."

Bacterial Methylphosphonate Degradation Potential

Bacterial methylphosphonate-degradation genes were associated with methane flux, supporting a predicted contribution to methane production in unrestored ponds. This node describes the bacterial evidence, not bacterial exclusivity: the study also recovered archaeal genomes with phnJ. Genomic potential and correlation do not measure this pathway's methane contribution or demonstrate cross-feeding between bacteria and methanogens.

Participating Taxa: unrestored salt pond methane-linked bacteria

Metabolites: methane (CHEBI:16183 · MediaIngredientMech · CMMMech)

Evidence

Salinity and Sulfate Associations with Methane Flux

Methane emissions were positively associated with salinity and sulfate across the sampled sites. These covarying field measurements do not demonstrate sulfate-driven methanogenesis, sulfate-reducer competition or niche partitioning. The source discusses possible environmental explanations, but this node retains only the observed association.

Metabolites: sulfate (CHEBI:16189 · MediaIngredientMech · CMMMech), methane (CHEBI:16183 · MediaIngredientMech · CMMMech)

Evidence

Knowledge gaps & discussions (1)

KNOWLEDGE_GAP OPEN What fraction of field methane derives from each inferred pathway, and which partner interactions are actually demonstrated?

The primary results, discussion and relevant statistical methods were read. Field covariation and genomic potential do not isolate interspecies exchange, product-removal feedback, competition or the causal effect of restoration. Microcosm substrate responses support community activity but do not apportion field flux among taxa/pathways. No prior correlation-based direction is restored. Broad non-graph guild roles and bottle-capacity/working-volume conflation remain tracked in #1814.

Attaches to: ecological_interactions#Restoration-State Community Composition Association, ecological_interactions#Archaeal Methanogenesis Evidence and Methane Flux Association, ecological_interactions#Bacterial Methylphosphonate Degradation Potential, ecological_interactions#Salinity and Sulfate Associations with Methane Flux

1 evidence item(s)
OTHER SUPPORT doi:10.1038/s41396-021-01067-w

These correlations should be interpreted cautiously, however, because the genes could be present but inactive in the methylotrophic methanogens

The source explicitly distinguishes gene presence/correlation from realized activity.

External Resources

Name Repository Resource ID
Primary publication for South Bay salt pond methane communities
ISME Journal article reporting 16S rRNA amplicon, shotgun metagenomic, methane flux, and sediment geochemistry analyses across unrestored, restored, and reference South Bay wetland sites. 		OTHER doi:10.1038/s41396-021-01067-w
DOE PAGES record
DOE PAGES record for the South Bay salt pond methane-emissions microbial community study. 		OTHER OSTI:1893114
Supplementary sample accession table
Supplementary table listing sample identifiers and accession information for 16S rRNA and metagenomic data; specific accessions are not repeated here because they were not verified individually during this pass. 		OTHER Table S1

Environmental Factors

Factor Value Unit
Restoration management state two unrestored salt ponds, restored salt pond, and reference wetland N/A
Salinity gradient salinity positively correlated with methane flux N/A
Sulfate concentration sulfate positively correlated with methane flux N/A
Methane flux elevated in unrestored salt ponds N/A

Growth Media

Pond R2 water with soil slurry, no substrate added (control)

Atmosphere ANAEROBIC

Preparation notes: Pond R2 water is the medium, not a formulation: it was equilibrated overnight in the anaerobic chamber to strip oxygen, then 10-15 mL of Pond R2 soil was slurried into 15 mL of it. Each bottle then received 15 mL of ONE substrate solution or pure medium, three replicates each (n = 12 total). The four treatments are recorded as four media because no bottle ever held more than one substrate; a single composition listing all three would describe a medium that never existed (#652). atmosphere is ANAEROBIC on the stated chamber gas mix, not inferred from habitat (cf. #644, #649). No chamber temperature is reported.

Evidence

doi:10.1038/s41396-021-01067-w

"Water collected from Pond R2 (unrestored) was used as a culture medium for a substrate addition incubation experiment."

doi:10.1038/s41396-021-01067-w

"The experiment was conducted in a Type B Vinyl Anaerobic Chamber (Coy Lab Products, Inc. Michigan) enriched with non-flammable hydrogen gas mixture (less than 5%), CO2 (5%), and N2 (balance)."

doi:10.1038/s41396-021-01067-w

"The hydrogen concentration is typically reduced down to 0.2−0.6% during oxygen scavenging and is not enough to support hydrogenotrophic methanogenesis."

doi:10.1038/s41396-021-01067-w

"After the water equilibrated overnight in the chamber to remove remaining oxygen, 10−15 mL of soil from an additional core collected from Pond R2 in March 2015 were mixed with 15 mL culture medium to make a soil slurry, which was funneled into autoclaved 100 mL glass bottles."

doi:10.1038/s41396-021-01067-w

"Fifteen milliliters solutions of trimethylamine (15 mM), methanol (20 mM), acetate (20 mM), or pure culture medium (control) were prepared and injected into the glass bottles with three replicates for each treatment (n = 12 total)."

doi:10.1038/s41396-021-01067-w

"CH4 production was measured with a Picarro G2508 Cavity Ringdown Spectrometer (Picarro, Inc. California) after substrate addition and every other day for two weeks."

Pond R2 water with soil slurry, amended with trimethylamine

Atmosphere ANAEROBIC

Composition

Component Concentration Unit CHEBI
trimethylamine · MediaIngredientMech 15 mM CHEBI:18139

Preparation notes: Pond R2 water is the medium, not a formulation: it was equilibrated overnight in the anaerobic chamber to strip oxygen, then 10-15 mL of Pond R2 soil was slurried into 15 mL of it. Each bottle then received 15 mL of ONE substrate solution or pure medium, three replicates each (n = 12 total). The four treatments are recorded as four media because no bottle ever held more than one substrate; a single composition listing all three would describe a medium that never existed (#652). atmosphere is ANAEROBIC on the stated chamber gas mix, not inferred from habitat (cf. #644, #649). No chamber temperature is reported.

Evidence

doi:10.1038/s41396-021-01067-w

"Water collected from Pond R2 (unrestored) was used as a culture medium for a substrate addition incubation experiment."

doi:10.1038/s41396-021-01067-w

"The experiment was conducted in a Type B Vinyl Anaerobic Chamber (Coy Lab Products, Inc. Michigan) enriched with non-flammable hydrogen gas mixture (less than 5%), CO2 (5%), and N2 (balance)."

doi:10.1038/s41396-021-01067-w

"After the water equilibrated overnight in the chamber to remove remaining oxygen, 10−15 mL of soil from an additional core collected from Pond R2 in March 2015 were mixed with 15 mL culture medium to make a soil slurry, which was funneled into autoclaved 100 mL glass bottles."

doi:10.1038/s41396-021-01067-w

"Fifteen milliliters solutions of trimethylamine (15 mM), methanol (20 mM), acetate (20 mM), or pure culture medium (control) were prepared and injected into the glass bottles with three replicates for each treatment (n = 12 total)."

Pond R2 water with soil slurry, amended with methanol

Atmosphere ANAEROBIC

Composition

Component Concentration Unit CHEBI
methanol · MediaIngredientMech 20 mM CHEBI:17790

Preparation notes: Pond R2 water is the medium, not a formulation: it was equilibrated overnight in the anaerobic chamber to strip oxygen, then 10-15 mL of Pond R2 soil was slurried into 15 mL of it. Each bottle then received 15 mL of ONE substrate solution or pure medium, three replicates each (n = 12 total). The four treatments are recorded as four media because no bottle ever held more than one substrate; a single composition listing all three would describe a medium that never existed (#652). atmosphere is ANAEROBIC on the stated chamber gas mix, not inferred from habitat (cf. #644, #649). No chamber temperature is reported.

Evidence

doi:10.1038/s41396-021-01067-w

"Water collected from Pond R2 (unrestored) was used as a culture medium for a substrate addition incubation experiment."

doi:10.1038/s41396-021-01067-w

"The experiment was conducted in a Type B Vinyl Anaerobic Chamber (Coy Lab Products, Inc. Michigan) enriched with non-flammable hydrogen gas mixture (less than 5%), CO2 (5%), and N2 (balance)."

doi:10.1038/s41396-021-01067-w

"After the water equilibrated overnight in the chamber to remove remaining oxygen, 10−15 mL of soil from an additional core collected from Pond R2 in March 2015 were mixed with 15 mL culture medium to make a soil slurry, which was funneled into autoclaved 100 mL glass bottles."

doi:10.1038/s41396-021-01067-w

"Fifteen milliliters solutions of trimethylamine (15 mM), methanol (20 mM), acetate (20 mM), or pure culture medium (control) were prepared and injected into the glass bottles with three replicates for each treatment (n = 12 total)."

Pond R2 water with soil slurry, amended with acetate

Atmosphere ANAEROBIC

Composition

Component Concentration Unit CHEBI
acetate · MediaIngredientMech 20 mM CHEBI:30089

Preparation notes: Pond R2 water is the medium, not a formulation: it was equilibrated overnight in the anaerobic chamber to strip oxygen, then 10-15 mL of Pond R2 soil was slurried into 15 mL of it. Each bottle then received 15 mL of ONE substrate solution or pure medium, three replicates each (n = 12 total). The four treatments are recorded as four media because no bottle ever held more than one substrate; a single composition listing all three would describe a medium that never existed (#652). atmosphere is ANAEROBIC on the stated chamber gas mix, not inferred from habitat (cf. #644, #649). No chamber temperature is reported.

Evidence

doi:10.1038/s41396-021-01067-w

"Water collected from Pond R2 (unrestored) was used as a culture medium for a substrate addition incubation experiment."

doi:10.1038/s41396-021-01067-w

"The experiment was conducted in a Type B Vinyl Anaerobic Chamber (Coy Lab Products, Inc. Michigan) enriched with non-flammable hydrogen gas mixture (less than 5%), CO2 (5%), and N2 (balance)."

doi:10.1038/s41396-021-01067-w

"After the water equilibrated overnight in the chamber to remove remaining oxygen, 10−15 mL of soil from an additional core collected from Pond R2 in March 2015 were mixed with 15 mL culture medium to make a soil slurry, which was funneled into autoclaved 100 mL glass bottles."

doi:10.1038/s41396-021-01067-w

"Fifteen milliliters solutions of trimethylamine (15 mM), methanol (20 mM), acetate (20 mM), or pure culture medium (control) were prepared and injected into the glass bottles with three replicates for each treatment (n = 12 total)."

Cross-Mech Suite Links

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

HabitatMech: former industrial salt pond sediment ↗ TaxonMech: South Bay salt pond sediment microbial communities ↗ TraitMech: South Bay salt pond sediment microbial communities ↗ TaxonMech: unrestored salt pond methane-linked bacteria ↗ TraitMech: unrestored salt pond methane-linked bacteria ↗ TaxonMech: salt pond methanogenic archaea ↗ TraitMech: salt pond methanogenic archaea ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗