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Coastal Forested Wetland Seawater-Ion Microcosm Community

Community ID CommunityMech:000258
Ecological State PERTURBED
Environment coastal forested freshwater wetland soil — ontology label: wetland area
ENVO:00000043 · HabitatMech ↗

A restored coastal forested freshwater wetland soil community from the Timberlake Observatory for Wetland Restoration in North Carolina, curated around a manipulative laboratory microcosm experiment that disentangled sulfate from other seawater ions. Intact wetland soil cores received deionized water, artificial seawater, artificial seawater without sulfate, or sulfate alone, followed by DNA sequencing, biogeochemical measurements, and greenhouse gas flux measurements. The experiment found that artificial seawater altered microbial richness, composition, functional genes, and emissions of carbon dioxide, methane, and nitrous oxide whether sulfate was present or absent, whereas sulfate alone did not alter emissions or enrich sulfate-reducing bacteria or sulfur cycling genes. The record is DOE-relevant because authors were affiliated with the DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, and sequencing followed DOE JGI methods.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
coastal forested wetland soil microbial community — ontology label: cellular organisms NCBITaxon:131567 · TaxonMech · TraitMech
PRIMARY_DEGRADER SECONDARY_FERMENTER SYNTROPHIC_PARTNER
N/A
  • PMID:38628812 - SUPPORT (IN_VITRO)
    "manipulative laboratory microcosm experiment"
  • PMID:38628812 - SUPPORT (COMPUTATIONAL)
    "combined with DNA sequencing and biogeochemical measurements"
coastal wetland sulfate-reducing bacteria — ontology label: Bacteria NCBITaxon:2 · TaxonMech · TraitMech
PRIMARY_DEGRADER SECONDARY_FERMENTER
N/A
  • PMID:38628812 - SUPPORT (COMPUTATIONAL)
    "sulfate reducing bacteria or sulfur cycling genes"
  • PMID:38628812 - SUPPORT (IN_VITRO)
    "addition of sulfate alone did not lead to increases in the abundance of sulfate reducing bacteria"
coastal wetland carbon nitrogen phosphorus cycling guilds — ontology label: cellular organisms NCBITaxon:131567 · TaxonMech · TraitMech
PRIMARY_DEGRADER SECONDARY_FERMENTER CROSS_FEEDER
N/A
  • PMID:38628812 - SUPPORT (COMPUTATIONAL)
    "genes involved in carbon, nitrogen, and phosphorus cycling responded more strongly to artificial seawater than to sulfate"

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 Coastal Forested Wetland Seawater-Ion Microcosm 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

Experimental Seawater-Ion Exposure

Soil-core microcosms from one acidic, restored freshwater wetland received deionized water, 5 ppt artificial seawater, artificial seawater without sulfate, or sulfate alone. The 12-week experiment separates sulfate and non-sulfate mixture effects. It does not isolate sodium chloride from all other ions or establish a universal coastal-field response.

Metabolites: sulfate (CHEBI:16189 · MediaIngredientMech · CMMMech), methane (CHEBI:16183 · MediaIngredientMech · CMMMech), carbon dioxide (CHEBI:16526 · MediaIngredientMech · CMMMech)

Biological Processes:

Downstream Effects:
→ Relative Carbon Nitrogen And Phosphorus Gene Abundances

The controlled ion mixtures altered relative DNA gene abundances at week 12, supporting a treatment effect on measured functional potential. PARTIAL - the responsible ions and biological mediators remain unresolved; this is not evidence of gene expression or activity changes.

→ Week-12 Greenhouse-Gas Flux Response

Controlled seawater-ion exposure changed week-12 whole-core net gas fluxes in treatment-specific comparisons. PARTIAL - factorial mixture effects and individual pairwise contrasts differ, and community composition or gene correlations do not establish the mediators of each gas response.

Evidence

  • PMID:38628812 - SUPPORT (IN_VITRO)
    "Greenhouse gas emissions and microbial richness and composition were altered by artificial seawater regardless of whether sulfate was present"
  • PMID:38628812 - PARTIAL (IN_VITRO)
    "other ions present in seawater, not sulfate, drive ecological and biogeochemical responses"

Week-12 Sulfate-Reduction Feature Response

Sulfate addition increased porewater sulfate but did not enrich the measured relative sulfate-reducer abundance or sulfate-reduction gene features at week 12. Hydrogen sulfide was detected in sulfate-amended water at day 14. The bounded abundance result therefore does not establish inactive sulfate reduction, reciprocal competition, or absence of all sulfate-only gas effects.

Metabolites: sulfate (CHEBI:16189 · MediaIngredientMech · CMMMech)

Biological Processes:

Evidence

  • PMID:38628812 - PARTIAL (IN_VITRO)
    "sulfate alone did not alter emissions or communities"
  • PMID:38628812 - SUPPORT (IN_VITRO)
    "addition of sulfate alone did not lead to increases in the abundance of sulfate reducing bacteria or sulfur cycling genes"

Relative Carbon Nitrogen And Phosphorus Gene Abundances

Shotgun DNA metagenomes showed relative abundances of carbon-, nitrogen- and phosphorus-cycling genes responding more strongly to artificial-seawater mixtures than sulfate alone. These are community functional-potential measurements, not transcript abundance, pathway activity or proof that the correlated genes mediate gas flux.

Metabolites: methane (CHEBI:16183 · MediaIngredientMech · CMMMech), carbon dioxide (CHEBI:16526 · MediaIngredientMech · CMMMech)

Biological Processes:

Evidence

  • PMID:38628812 - SUPPORT (COMPUTATIONAL)
    "genes involved in carbon, nitrogen, and phosphorus cycling responded more strongly to artificial seawater than to sulfate"

Week-12 Greenhouse-Gas Flux Response

Week-12 whole-core net CO2, CH4 and N2O fluxes were measured. CO2 had a significant overall treatment and non-sulfate-factor effect but no significant individual pairwise contrasts. CH4 was higher without sulfate than in the water control or sulfate-only treatment; complete artificial seawater was intermediate. N2O was lower in every amended arm, including sulfate-only, than in the control. These outcomes do not directly partition microbial production and consumption pathways.

Metabolites: methane (CHEBI:16183 · MediaIngredientMech · CMMMech), carbon dioxide (CHEBI:16526 · MediaIngredientMech · CMMMech)

Biological Processes:

Evidence

  • PMID:38628812 - SUPPORT (IN_VITRO)
    "emissions of carbon dioxide, methane, and nitrous oxide"
  • PMID:38628812 - PARTIAL (IN_VITRO)
    "may be drivers of increased methane emissions in soils that received artificial seawater addition"

Knowledge gaps & discussions (1)

KNOWLEDGE_GAP OPEN Which ions and microbial processes mediate the treatment-specific net gas responses?

Controlled ion-mixture exposure supports causal treatment effects, but not isolated sodium chloride action. Relative DNA gene counts and guild correlations do not measure activity or establish mediation. Selective ion and pathway interventions with production/consumption measurements would resolve mechanisms. Week-12 gene features and day-14 water chemistry must remain separate; the sulfate-only N2O contrast prevents an unqualified no-gas-effect claim.

Attaches to: ecological_interactions#Experimental Seawater-Ion Exposure, ecological_interactions#Week-12 Sulfate-Reduction Feature Response, ecological_interactions#Relative Carbon Nitrogen And Phosphorus Gene Abundances, ecological_interactions#Week-12 Greenhouse-Gas Flux Response

External Resources

Name Repository Resource ID
Primary publication for coastal forested wetland seawater-ion microcosms
PubMed record for the ISME Communications article on sulfate and non-sulfate seawater ion effects on microbial communities and greenhouse gas emissions in a coastal forested wetland microcosm. 		OTHER PMID:38628812
  • PMID:38628812 - SUPPORT (OTHER)
    "Disentangling the effects of sulfate and other seawater ions"
DOI landing page
DOI for the ISME Communications publication. 		OTHER doi:10.1093/ismeco/ycae040
PubMed Central full text
Open-access full text with methods and discussion for the seawater-ion wetland microcosm study. 		OTHER PMCID:PMC11020224
  • PMID:38628812 - SUPPORT (OTHER)
    "Department of Energy Joint Genome Institute"

Environmental Factors

Factor Value Unit
Seawater intrusion simulation artificial seawater, artificial seawater without sulfate, sulfate only, and deionized-water control N/A
  • PMID:38628812 - SUPPORT (IN_VITRO)
    "tease apart the effects of sulfate from other seawater ions"
Coastal wetland salinization salt water components altering microbial community composition and function N/A
  • PMID:38628812 - SUPPORT (IN_VITRO)
    "consequences of coastal wetland salinization"
Greenhouse gases carbon dioxide, methane, and nitrous oxide N/A
  • PMID:38628812 - SUPPORT (IN_VITRO)
    "emissions of carbon dioxide, methane, and nitrous oxide"

Growth Media

artificial seawater (Kester et al. recipe) at 5 ppt, and its sulfate-free and sulfate-only variants

Composition

Component Concentration Unit CHEBI
sodium chloride · MediaIngredientMech 3.421 g/L CHEBI:26710
potassium sulfate · MediaIngredientMech 0.573 g/L CHEBI:32036
potassium chloride · MediaIngredientMech 0.097 g/L N/A
sodium bicarbonate · MediaIngredientMech 0.028 g/L CHEBI:32139
potassium bromide · MediaIngredientMech 0.001 g/L N/A
boric acid · MediaIngredientMech 0.004 g/L N/A
sodium fluoride · MediaIngredientMech 0.429 mg/L N/A
magnesium chloride hexahydrate (1 M stock) · MediaIngredientMech 8.15 mL/L N/A
calcium chloride dihydrate (1 M stock) · MediaIngredientMech 1.601 mL/L N/A
strontium chloride hexahydrate (0.1 M stock) · MediaIngredientMech 0.13 mL/L N/A

Preparation notes: Four treatments: deionized water (control), artificial seawater (+ASW), ASW without sulfate (+ASW-SO4) and sulfate only (+SO4). In +ASW-SO4 the omitted K2SO4 was replaced with equivalent additional NaCl and KCl, which is what isolates the sulfate effect from the other seawater ions. The composition above is the full +ASW medium. NO INCUBATION TEMPERATURE, pH, LIGHT REGIME OR ATMOSPHERE IS REPORTED in the source, so those fields are left unset rather than inferred. The cores were fitted with a gas-tight lid only to measure fluxes, so they were not held under a defined headspace and `atmosphere` is unset rather than ANAEROBIC (#644); the cores are the growth substrate and the inoculum together, so there is no separate formulated growth medium.

Evidence

PMID:38628812

"Laboratory microcosms were started with intact soil cores 2.5 cm in diameter and 30-cm deep, which then received either deionized water (control), artificial seawater (+ASW), artificial seawater without sulfate (+ASW-SO4), and sulfate only (+SO4)."

PMID:38628812

"adjusted to 5-ppt salinity. The recipe (in g/L unless otherwise stated) was as follows: 3.421 NaCl, 0.573 K2SO4, 0.097 KCl, 0.028 NaHCO3, 0.001 KBr, 0.004 H3BO3, 0.429 mg/L NaF, 8.15 mL MgCl2-6H2O (1 M), 1.601 mL CaCl2-2H2O (1 M), 0.130 mL SrCl2-6H2O (0.1 M)."

PMID:38628812

"In the ASW-SO4 treatment, the absent K2SO4 was replaced with an equivalent amount of additional NaCl and KCl."

PMID:38628812

"Soil cores were collected in 2011 from the Timberlake Observatory for Wetland Restoration in North Carolina, USA (35°54′22′′ N, 76°09′25′′ W, 0-m elevation), a forested freshwater wetland in the Alligator River estuary that connects to the Albemarle Sound."

PMID:38628812

"The collection site is characterized by Eutric Histosol soils and Atlantic white cedar vegetation"

PMID:38628812

"The experiment proceeded for 12 weeks, after which soils from 0- to 5-cm depth and 10- to 15-cm depth profiles were collected, a portion stored at −20°C for DNA sequencing, and another aliquot analyzed for porewater and soil biogeochemistry."

Cross-Mech Suite Links

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

HabitatMech: coastal forested freshwater wetland soil ↗ TaxonMech: coastal forested wetland soil microbial community ↗ TraitMech: coastal forested wetland soil microbial community ↗ TaxonMech: coastal wetland sulfate-reducing bacteria ↗ TraitMech: coastal wetland sulfate-reducing bacteria ↗ TaxonMech: coastal wetland carbon nitrogen phosphorus cycling guilds ↗ TraitMech: coastal wetland carbon nitrogen phosphorus cycling guilds ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗