An autotrophic biofilm community in sulfide-rich springs sustained by deeply sourced groundwater. Genome-resolved metagenomics combined with bulk geochemistry and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K reveals biofilms dominated by chemolithotrophic sulfur-oxidizing bacteria including Thiothrix and Beggiatoa, with diverse Candidate Phyla Radiation (CPR) bacteria (Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, Parcubacteria). STXM imaging shows ultra-small cells adhered near filamentous bacteria, suggesting CPR episymbiosis. Carbon K and sulfur L2,3 edge NEXAFS spectroscopy indicates that filamentous bacteria contain protein-encapsulated elemental sulfur granules consistent with Thiothrix-like sulfur oxidation, and Berkelbacteria and Moranbacteria are predicted to encode a novel electron bifurcation system.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Thiothrix | NCBITaxon:1030 · TaxonMech · TraitMech |
PRIMARY_PRODUCER
PRIMARY_DEGRADER
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DOMINANT |
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| Beggiatoa-related Gammaproteobacteria (unresolved genus) — ontology label: Gammaproteobacteria | NCBITaxon:1236 · TaxonMech · TraitMech |
PRIMARY_PRODUCER
PRIMARY_DEGRADER
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DOMINANT |
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| Candidate Phyla Radiation (CPR) bacteria — ontology label: Patescibacteria group | NCBITaxon:1783273 · TaxonMech · TraitMech |
SYNTROPHIC_PARTNER
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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.
Filamentous Sulfur Oxidation with Encapsulated S Granules
STXM and sulfur-edge spectroscopy show protein-associated elemental sulfur granules in filaments from the MS4 and MS11 spring biofilms, consistent with sulfur oxidation. Primary Table S4 supports Thiothrix genus attribution for the named MS4 bin, with no species assignment. HYPOTHESIZED/PARTIAL: this is not identification of the imaged cells; Thiothrix nivea is not established. The Beggiatoa-related canonical participant remains unresolved below class: its explicit Gammaproteobacteria parent anchor preserves the source group's presence without assigning the bins to Beggiatoa or identifying the imaged filaments. Primary Table S4 leaves genus blank. These observations do not demonstrate commensalism or neutral effects on a host.
Participating Taxa: Thiothrix, Beggiatoa-related Gammaproteobacteria (unresolved genus)
Metabolites: sulfide (CHEBI:15138 · MediaIngredientMech · CMMMech), elemental sulfur (CHEBI:26833 · MediaIngredientMech · CMMMech)
Biological Processes:
- sulfur compound metabolic process (GO:0006790 · PathwayMech)
Evidence
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PMID:38273328 - PARTIAL (IN_VIVO)"filamentous bacteria contain protein-encapsulated spherical elemental sulfur granules, indicating that they are sulfur oxidizers, likely Thiothrix"
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PMID:38273328 - SUPPORT (COMPUTATIONAL)"Genomically represented groups in the biofilms and planktonic fractions from both sites include Gammaproteobacteria (Thiotrichales, Chromatiales, Beggiotales)"
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PMID:38273328 - SUPPORT (COMPUTATIONAL)"d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix;s__"
Putative CPR association with sulfur-oxidizing filaments
HYPOTHESIZED/PARTIAL: small cells occur near or on sulfur-bearing filaments, and the authors propose that some are CPR episymbionts. Attempts to identify CPR cells by FISH were unsuccessful, so the observed cells, their hosts and the fitness consequences remain unresolved. The target now uses the source-supported Thiothrix genus rather than an unsupported species. These source/target links do not verify a CPR-Thiothrix pair. A possible cryptic sulfur-cycling symbiosis remains a source hypothesis, not demonstrated exchange.
Source Taxon: Candidate Phyla Radiation (CPR) bacteria
Target Taxon: Thiothrix
Biological Processes:
- interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
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PMID:38273328 - PARTIAL (IN_VIVO)"STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts"
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PMID:38273328 - SUPPORT (IN_VIVO)"our attempts to perform fluorescent in situ hybridization to determine CPR bacterial identity were unsuccessful due to low amount of material, so this inference remains tentative."
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PMID:38273328 - SUPPORT (COMPUTATIONAL)"d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiothrix;s__"
Predicted CPR sulfur and hydrogen metabolic capacity
HYPOTHESIZED/PARTIAL: metagenomic gene content, genomic context and structural models suggest a potentially electron-bifurcating group 3b hydrogenase in Berkelbacteria/Moranbacteria and thiosulfate-conversion capacity in Doudnabacteria. These are lineage-specific predictions, not demonstrated enzyme activity, sulfur/hydrogen flux or a capacity shared by every CPR member. The authors suggest that such capacities could contribute to cryptic sulfur symbioses; neither a particular host nor metabolite exchange was experimentally resolved.
Participating Taxa: Candidate Phyla Radiation (CPR) bacteria
Metabolites: dihydrogen (CHEBI:18276 · MediaIngredientMech · CMMMech), thiosulfate (CHEBI:26977 · MediaIngredientMech · CMMMech), sulfite (CHEBI:17359 · MediaIngredientMech · CMMMech)
Biological Processes:
- sulfur compound metabolic process (GO:0006790 · PathwayMech)
Evidence
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PMID:38273328 - PARTIAL (COMPUTATIONAL)"Berkelbacteria and Moranbacteria in the same biofilm sample are predicted to have a novel electron bifurcating group 3b"
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PMID:38273328 - PARTIAL (COMPUTATIONAL)"One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that may convert thiosulfate to sulfite."
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Can the Beggiatoa-related bins be reconciled below their shared parent class, and can the imaged cells and metabolic coupling be identified?
Table S4 resolves the MS4 Thiothrix bin to genus, not species, consistent with the reported 51% average amino-acid similarity to T. nivea. Canonical taxonomy and both Thiothrix graph links use NCBITaxon:1030. The Beggiatoa-related roster entry and graph participant now share the explicit NCBITaxon:1236 Gammaproteobacteria parent anchor. Table S4 rows5/69 assign Beggiatoaceae but no genus/species; rows12/68 also lack family. This parent-rank repair does not equate GTDB Beggiatoaceae with NCBI Thiotrichaceae or settle the lower-rank identity. The source's Beggiatoa wording is retained in evidence. FISH did not resolve CPR identity, and proximity does not establish metabolic exchange. Issue #1841 and needs_research remain open. Non-graph functional-role and ingredient assertions remain outside this partial identity repair.
Attaches to: ecological_interactions#Filamentous Sulfur Oxidation with Encapsulated S Granules, ecological_interactions#Putative CPR association with sulfur-oxidizing filaments, ecological_interactions#Predicted CPR sulfur and hydrogen metabolic capacity
2 evidence item(s)
our attempts to perform fluorescent in situ hybridization to determine CPR bacterial identity were unsuccessful due to low amount of material, so this inference remains tentative.
States the unresolved identification boundary directly.
The most abundant species in MS4 shares genome-wide average 51% amino acid similarity with the sulfur-oxidizer Thiothrix nivea
The source describes similarity to a reference species, not identity as that species.
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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Primary publication for the autotrophic sulfide-spring CPR biofilm
PubMed record for the Valentin-Alvarado et al. 2024 Microbiome paper on sulfide-spring biofilms hosting diverse CPR bacteria. |
OTHER | PMID:38273328 |
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DOI landing page
DOI link to the Microbiome paper. |
OTHER | doi:10.1186/s40168-023-01704-w |
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Sulfide-rich groundwater | deeply sourced sulfide-rich spring water | N/A |
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