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 | NCBITaxon:131567 |
PRIMARY_DEGRADER
SECONDARY_FERMENTER
SYNTROPHIC_PARTNER
|
N/A |
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| unrestored salt pond methane-linked bacteria | NCBITaxon:2 |
PRIMARY_DEGRADER
|
N/A |
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| salt pond methanogenic archaea | NCBITaxon:2157 |
SYNTROPHIC_PARTNER
|
COMMON |
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Ecological Interactions
Restoration-State Niche Filtering
NICHE_PARTITIONINGEvidence
-
doi:10.1038/s41396-021-01067-w - SUPPORT (COMPUTATIONAL)"restored salt pond harbored communities more phylogenetically and functionally similar"
-
doi:10.1038/s41396-021-01067-w - SUPPORT (COMPUTATIONAL)"restoration effectively converted industrial salt pond microbial communities"
Archaeal Methanogenesis Coupled to Methane Flux
SYNTROPHYSource Taxon: salt pond methanogenic archaea
Metabolites: methane (CHEBI:16183)
Biological Processes:
- methanogenesis (GO:0015948)
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 (COMPUTATIONAL)"methane is generated both from bacterial methylphosphonate degradation and archaeal methanogenesis"
Bacterial Methylphosphonate Methane Pathway
CROSS_FEEDINGSource Taxon: unrestored salt pond methane-linked bacteria
Metabolites: methane (CHEBI:16183)
Evidence
-
doi:10.1038/s41396-021-01067-w - SUPPORT (COMPUTATIONAL)"genes encoding enzymes for bacterial methylphosphonate degradation"
-
doi:10.1038/s41396-021-01067-w - SUPPORT (COMPUTATIONAL)"methane is generated both from bacterial methylphosphonate degradation and archaeal methanogenesis"
Sulfate and Methanogenesis Competition
NICHE_PARTITIONINGMetabolites: sulfate (CHEBI:16189), methane (CHEBI:16183)
Biological Processes:
- methanogenesis (GO:0015948)
Evidence
-
doi:10.1038/s41396-021-01067-w - SUPPORT (IN_VIVO)"positively correlated with salinity and sulfate across all samples"
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 |
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DOE PAGES record
DOE PAGES record for the South Bay salt pond methane-emissions microbial community study. |
OTHER | OSTI:1893114 |
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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 |
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Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Restoration management state | two unrestored salt ponds, restored salt pond, and reference wetland | N/A |
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| Salinity gradient | salinity positively correlated with methane flux | N/A |
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| Sulfate concentration | sulfate positively correlated with methane flux | N/A |
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| Methane flux | elevated in unrestored salt ponds | N/A |
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