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Organism in Subsurface and Soil Community Ecology

Geobacter

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Sources cited
2 project reports and 1 cross-project digest, listed in the margin
Linked from
4 pages1 topic

Geobacter is a bacterial genus that this corpus treats as an iron reducer. In the cited literature, it and Geothrix (geothrix) are the signature lineages of rock-attached Opalinus clay communities. 1,2

Mont Terri: porewater versus rock surfaces

At mont-terri, two literature paradigms describe qualitatively different microbial communities at the same clay site. The Bagnoud (2016) Opalinus porewater paradigm describes porewater dominated by sulfate reducers (dissimilatory-sulfate-reduction). The Mitzscherling (2023) rock-attached paradigm describes rock surfaces dominated by Geobacter/Geothrix iron reducers. The corpus records this as a contrast between habitats within one site. It is not a disagreement about a single community. 1

The Mitzscherling et al. (2023) rock-attached community profile reports sulfate-reducing bacteria (SRB) at <0.2% and iron-reducing bacteria (IRB) at 4.3–10.2%, dominated by Geobacter and Geothrix. In the clay_confined_subsurface project this profile is only a literature comparator. It is not an iron-marker result measured in that project’s cultured-genome cohort. 2

Caveat: rock-attached Geobacter/Geothrix lineages are essentially absent from the genome cohort that clay_confined_subsurface analysed. CPR/DPANN episymbionts (Bell 2022) are also essentially absent. The project therefore could not test the rock-attached iron-reducer paradigm directly. The report states that MAG-augmented future work is needed to test whether the genuine clay-confined community matches the literature predictions. MAGs are metagenome-assembled genomes reconstructed from environmental sequencing. 2

ENIGMA groundwater versus sediment

In the ENIGMA ASV ecology analysis, the source table reports abundances as percentages in two columns, “Sediment %” and “GW %” (GW is groundwater), followed by a fold enrichment. All pairs below are listed as Sediment % / GW %. Geobacter (iron reduction) is 0.00 / 0.01, with a 5.5× ▲GW enrichment. Because these percentages are very small, the fold enrichment rests on trace abundances. The other iron-cycling genera show different patterns. The iron oxidizers gallionella (0.01 / 0.14, 8.9× ▲GW) and sideroxydans (0.01 / 0.06, 7.0× ▲GW) are also enriched in groundwater. In contrast, the iron/U reducer anaeromyxobacter (1.24 / 0.03, 0.02× ▼GW) is depleted in groundwater. For comparison, rhodanobacter (denitrification) is 1.23 / 3.62 (2.9× ▲GW), arcobacter (sulfur oxidation) is 0.54 / 0.00 (0× ▼GW), and Ca. methanoperedens (methane oxidation) is 0.42 / 0.00 (0× ▼GW). 3

Sources cited

  1. Discoveries Logdiscoveries · cited 4× · cross-project digest · primary source
  2. Self-Sufficiency, Anaerobic Toolkit, and Cultivation Bias in Clay-Confined Cultured Bacterial Genomesclay_confined_subsurface · cited 4×
  3. SSO Subsurface Community Ecology — Spatial Structure, Functional Gradients, and Hydrogeological Driversenigma_sso_asv_ecology · cited 3×