Actinomyces naeslundii AK6 and Streptococcus mitis SK24 formed visible coaggregates in diluted Todd-Hewitt broth within 15 min, indicating a direct cell-cell association that can contribute to mixed-species early dental biofilm assembly.
+A. naeslundii AK6 and S. mitis SK24 formed visible coaggregates within 15 min in a separate planktonic assay in 1/10 Todd-Hewitt broth. This is direct physical association, not a demonstrated directional benefit, colonization-facilitation effect or cause of acidification in the five-species biofilm. The authors propose an adhesion contribution but did not selectively perturb coaggregation in the pH assay.
Source Taxon: Actinomyces naeslundii
@@ -692,28 +686,7 @@Biological Processes:
-Direct A. naeslundii-S. mitis coaggregation contributes to assembly of the reproducible five-species biofilm that was challenged with glucose for microscale pH imaging.
-Actinomyces naeslundii AK6 also coaggregated with Streptococcus sanguinis SK150, forming small suspended aggregates within 2 h and providing a second direct pairwise attachment interaction in the five-member biofilm.
+A. naeslundii AK6 and S. sanguinis SK150 formed small suspended aggregates within 2 h in the separate planktonic assay, weaker than the A. naeslundii-S. mitis association. The source/target fields identify the measured pair, not a direction of facilitation. This does not establish an attachment route or acidification mechanism in the five-species flow biofilm.
Source Taxon: Actinomyces naeslundii
@@ -755,29 +727,8 @@Direct A. naeslundii-S. sanguinis coaggregation provides a second attachment route into the five-species biofilm whose glucose metabolism generated stable acidic microenvironments.
-After the five species were established as a reproducible flow-channel biofilm, glucose addition immediately triggered biofilm acid production and generated stable extracellular pH microenvironments at the biofilm-substrate interface.
+Sequentially assembled five-species plastic flow-channel biofilms showed extracellular acidification after 0.4% or 10% glucose in sterile saliva, while the no-glucose control remained above pH 7. Spatial pH differences persisted for hours. This is a collective glucose-response endpoint, not demonstrated niche partitioning, metabolite exchange, species-specific acid flux or enamel demineralization. Growth in flowing diluted Todd-Hewitt broth and the later salivary glucose challenge are distinct stages.
+ + + +Participating Taxa: + Streptococcus oralis, + Streptococcus sanguinis, + + Streptococcus mitis, + + Streptococcus downei, + + Actinomyces naeslundii + +
@@ -862,6 +826,25 @@Planktonic coaggregation and glucose-responsive biofilm pH were measured in different assays. Neither pair was selectively disrupted or rescued in the biofilm; physical association does not establish colonization benefit or mediation of the pH response. Resolve species-specific acid flux and the origin of persistent pH heterogeneity experimentally. The two workflow-to-outcome arrows are removed. Flow rate, growth feed, substrate and temperature-stage metadata remain under #1420.
+ +Attaches to: ecological_interactions#A. naeslundii and S. mitis Planktonic Coaggregation, ecological_interactions#A. naeslundii and S. sanguinis Planktonic Coaggregation, ecological_interactions#Five-species glucose acidification of the biofilm interface
High-prevalence floodplain genomes form a shared reservoir of one-carbon, sulfur, nitrogen, hydrogen, and aerobic respiratory capacity that becomes active as environmental conditions change across East River floodplain soils.
+The 2015 operational core comprises 42 representative genomes detected in at least 89 of 94 samples without a significant association to any one floodplain. Their gene inventories define biogeochemical potential, not measured activation or flux. Listed Betaproteobacteria and Gemmatimonadota participants are partial higher-level core groupings, not a complete roster or an assertion that every genome encodes every pathway. Widely represented capacities did not predict the later transcription snapshot.
+Participating Taxa: + + Betaproteobacteria-dominated core floodplain microbiome, + + Gemmatimonadota floodplain representatives + +
+Metabolites: @@ -715,25 +722,23 @@
Shared core genomes encode aerobic respiration, aerobic carbon monoxide oxidation, and thiosulfate oxidation capacity across meanders.
-The core capacity reservoir is expressed unevenly; under lower soil organic carbon, chemolithotrophic one-carbon, sulfur, hydrogen, and nitrogen redox genes become highly active.
-The cross-site core floodplain microbiome is enriched in aerobic respiration, carbon monoxide oxidation, and thiosulfate oxidation, indicating shared redox capacity across meander-bound floodplain soils.
+The operational core genome set is enriched in capacities for aerobic respiration, aerobic CO or other small-molecule oxidation, and thiosulfate oxidation. This is comparative gene-content enrichment, not measured reaction rates, cooperation or niche partitioning. The two canonical participant groups are a partial core roster; no universal per-taxon pathway assignment or substrate specificity for every CODH-like homolog is implied.
+Participating Taxa: + + Betaproteobacteria-dominated core floodplain microbiome, + + Gemmatimonadota floodplain representatives + +
+Metabolites: @@ -817,14 +829,19 @@
Floodplain soils with lower organic carbon show increased activity of genes for methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, nitrate and nitrite reduction, and carbon fixation, suggesting functional niche shifts along carbon gradients.
+In the September 2016 floodplain L RNA snapshot, lower organic carbon correlated with increased transcription of selected C1, sulfur, hydrogen and nitrogen redox genes and carbon-fixation genes. This is not a carbon manipulation, measured flux, a result independently sampled in all three floodplains or activation of the entire 2015 core. Betaproteobacteria are included only as a broad grouping linked to CBB carbon-fixation capacity/activity; their overall transcription favored higher organic carbon. Other low-carbon-active groups are not reliably represented by the canonical taxonomy, so this is explicitly a partial participant list.
+Participating Taxa: + + Betaproteobacteria-dominated core floodplain microbiome + +
+Metabolites: @@ -871,7 +888,7 @@
Core capacity enrichment is a part/whole description, not a causal consequence requiring an arrow. Gene inventories did not predict one-time expression, and the 2016 RNA study sampled only L. Direct flux and selective environmental perturbations are missing. The canonical Nitrospira genus ID cannot stand in for the paper's Nitrospirae phylum; Acidobacteriota are non-core and overall more transcriptionally active at higher organic carbon. Neither is assigned an unsupported graph link just to suppress disconnected warnings. Taxonomy and non-graph scope remain under #1421; no GTDB withholding policy is changed.
+ +Attaches to: ecological_interactions#Core Floodplain Biogeochemical Potential Reservoir, ecological_interactions#Core Floodplain Aerobic and Sulfur Oxidation Capacity, ecological_interactions#Low-Organic-Carbon-Associated Gene Transcription in Floodplain L
Proximity to the stream, groundwater table, and weathered shale strongly structures community composition and metabolic potential along the hillslope-to-riparian transect.
+Across the September 2016 PLM transect, microbial composition and DNA-based metabolic potential covaried with depth, river proximity, groundwater and weathered shale. HYPOTHESIZED moisture, redox and substrate filtering may explain these patterns, but no selective groundwater, shale or nutrient perturbation isolated the drivers. Compartment participants retain distinct canonical labels despite sharing a broad cellular-organisms ID; they are not resolved taxa.
+Participating Taxa: + + East River hillslope-riparian transect microbiome, + + riparian zone microbial communities, + + hillslope microbial communities + +
+Metabolites: @@ -718,18 +727,18 @@
Groundwater saturation and weathered shale stratify the transect into floodplain niches where carbon, nitrogen, and sulfur pathway genes differentiated riparian communities from hillslope communities.
+ → Riparian Carbon Nitrogen and Sulfur Genomic Potential +HYPOTHESIZED - groundwater-associated low-redox conditions may favor organisms carrying anaerobic carbon, nitrogen and sulfur pathway genes, producing the observed riparian-versus-hillslope differences. Spatial gene abundance supports the model but does not isolate redox as the mediator or demonstrate flux.
The same depth and saturation gradient that separates PLM4 water-table samples localizes CPR bacteria primarily to floodplain and groundwater-saturated sediments.
+HYPOTHESIZED - depth and water-table conditions may select compatible microorganisms and possible hosts, influencing candidate-phylum distributions. Observational detections support environmental filtering, but no host dependence or exclusive groundwater requirement was tested; deep hillslope exceptions remain.
Weathered shale and saturated sediments expose communities to mobilized selenium and the below-water-table redox conditions where srdA selenate-reductase genes were enriched.
+ → Deep Shale and Riparian Selenate Reduction Potential +HYPOTHESIZED - shale-derived selenium availability together with periodically reducing groundwater conditions may select selenate-respiring organisms and enrich srdA. Gene abundance and incomplete chemistry support this proposed mechanism, not experimentally demonstrated selenium reduction or export control.
Riparian-zone communities differ from hillslope communities in capacities for carbon fixation, nitrogen fixation, and sulfate reduction, suggesting that riparian saturated soils and sediments act as a biogeochemical functional zone in the watershed.
+Riparian samples near and below the water table differed from hillslope samples in DNA abundances of genes associated with carbon fixation, nitrogen fixation and sulfur reduction. DsrD and other reductase signatures help interpret direction, but RNA was extracted for another study and no pathway flux was measured here. This comparison supports a putative functional zone, not demonstrated interspecies niche partitioning, complete redox cycling or equivalent metabolism in all compartments.
+Participating Taxa: + + riparian zone microbial communities, + + hillslope microbial communities + +
+Metabolites: @@ -864,6 +880,19 @@
Bacteria from phyla lacking isolated representatives increase in abundance with depth, and CPR bacteria were detected in saturated riparian sediments, linking vertical hydrologic gradients to uncultivated bacterial community structure.
+Non-CPR candidate phyla increased with sampling depth. CPR detections were concentrated near and below the PLM4 water table, with two Yanofskybacteria occurrences in deep hillslope samples near weathered shale. These are distinct patterns, not exclusive confinement of every uncultivated lineage to saturated riparian sediment. CPR dependency on unknown hosts is a literature-based hypothesis, not measured cross-feeding or syntrophy in this transect.
-Source Taxon: riparian saturated sediment Candidate Phyla Radiation bacteria
+Participating Taxa: + East River hillslope-riparian transect microbiome, + riparian saturated sediment Candidate Phyla Radiation bacteria +
-Biological Processes:
-Selenium reduction is prominent at depth in weathered shale and saturated riparian sediments, indicating a water-quality-relevant redox function associated with the deeper transect microbiome.
+DNA abundance of the srdA catalytic-subunit gene was elevated in groundwater-saturated riparian samples and deep weathered shale, consistent with selenate-reduction potential. The measured srdA-selenium association lacks chemistry at the deepest high-srdA sites. Actual selenate reduction rates, selenium removal, growth support and water-quality improvement were not measured; this is not direct evidence of selenite reduction by a named taxon.
+ + +Participating Taxa: + riparian zone microbial communities, + + hillslope microbial communities + +
@@ -1057,6 +1100,25 @@Selective groundwater/redox/substrate perturbations and direct flux measurements are needed to distinguish the proposed drivers. DNA abundance is metabolic potential, not transcription or activity; selenium chemistry is missing at key deep high-srdA sites. CPR partners and exchanges are unknown, and candidate phyla are not synonymous with CPR. The three original arrows remain explicit hypotheses, not niche-partitioning facts. Non-graph role and activity wording remain under #1422.
+ +Attaches to: ecological_interactions#Hypothesized Groundwater and Weathered Shale Filtering, ecological_interactions#Riparian Carbon Nitrogen and Sulfur Genomic Potential, ecological_interactions#Depth-Enriched Uncultivated Bacterial Lineages, ecological_interactions#Deep Shale and Riparian Selenate Reduction Potential