Five parallel 2 L sequencing batch reactors enriched from municipal activated sludge under an aerobic dynamic feeding regime, each on a single volatile fatty acid or lactate as sole carbon source, and followed for 145 days by paired metagenomics and metatranscriptomics. The polyhydroxyalkanoate-producing mixed microbial cultures (PHA-MMCs) include dominant Azoarcus, Paracoccus, Azomonas, Thauera, and Brevundimonas populations across the different reactors. The study recovered 963 metagenome-assembled genomes and 4,294 phage operational taxonomic units. Bacterial and phage community turnover are statistically associated. Structural equation modeling estimates a negative association of phage abundance with bacterial alpha diversity and activity. The authors propose kill-the-winner predation as an explanation for alternating dominance; this is a model-inferred mechanism, not a controlled phage perturbation or direct demonstration of host lysis. Predicted host links and defense systems are sequence-derived. Predicted phage auxiliary metabolic genes are transcribed, but transcription does not establish a contribution to PHA yield or productive lytic infection. This many-phages-on-many-bacteria system complements the experimentally manipulated four-species community in CommunityMech:000467. The two records preserve the distinction between inferred phage effects and experimental intervention.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Azoarcus | NCBITaxon:12960 · TaxonMech · TraitMech | DOMINANT | |
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| Paracoccus — ontology label: Paracoccus <a-proteobacteria> | NCBITaxon:265 · TaxonMech · TraitMech | DOMINANT | |
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| Azomonas | NCBITaxon:69961 · TaxonMech · TraitMech | DOMINANT | |
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| Thauera | NCBITaxon:33057 · TaxonMech · TraitMech | DOMINANT | |
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| Brevundimonas | NCBITaxon:41275 · TaxonMech · TraitMech | DOMINANT | |
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| PHA-MMC phage community (4,294 pOTUs) — ontology label: Viruses | NCBITaxon:10239 · TaxonMech · TraitMech | 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.
Hypothesized Kill-the-Winner Succession of Dominant PHA Producers
KILL_THE_WINNERHYPOTHESIZED: the authors interpret alternating dominant species and the fitted SEM as consistent with phages lysing dominant hosts and freeing niches for successors. The succession pattern was observed during maintenance under constant aerobic dynamic feeding selection, but the mechanism is model-inferred rather than established by a phage manipulation or lysis assay. The KILL_THE_WINNER label denotes this explicitly qualified hypothesis.
Biological Processes:
- viral process (GO:0016032 · PathwayMech)
Evidence
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PMID:40152616 - PARTIAL (COMPUTATIONAL)"Structural equation modeling analysis showed that phages could infect and lyse dominant species to vacate ecological niches for other species, resulting in a community succession state in which dominant species alternated."
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PMID:40152616 - PARTIAL (COMPUTATIONAL)"Sample points in each reactor did not cluster together during the late stages of maintenance (days 65, 68, and 145), suggesting that the bacterial community structure reached alternative states during maintenance, even when deterministic selection pressure was applied"
Coupled Turnover of Phage and Bacterial Community Structure
Temporally adjacent samples were compared by Bray-Curtis dissimilarity for both the bacterial and the phage community, and the two turnover series track each other closely in all five reactors (Spearman rho 0.95, 0.77, 0.87, 0.99, and 0.80). Structural equation modelling returns a positive association between phage and bacterial community composition. This statistical association does not establish infection or causal direction.
Evidence
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PMID:40152616 - SUPPORT (COMPUTATIONAL)"There was a significant positive relationship between the bacterial and phage communities shifts"
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PMID:40152616 - PARTIAL (COMPUTATIONAL)"the dynamics of bacterial community structure could be mirrored in phage communities"
Modeled Association of Phage Abundance with Bacterial Diversity and Activity
Structural equation modeling estimates negative associations of phage abundance with bacterial alpha diversity (Chao1, r = -0.43, P <= 0.05) and bacterial community activity (r = -0.36). The authors interpret these associations as consistent with virulent phage effects. The modeled direction is not an experimental demonstration of host killing and does not exclude host-driven or other explanations.
Evidence
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PMID:40152616 - SUPPORT (COMPUTATIONAL)"significant negative correlation (r: −0.43, P ≤ 0.05) between phage abundance and the alpha diversity (Chao1) index of the bacterial community"
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PMID:40152616 - PARTIAL (COMPUTATIONAL)"the SEM was used to discern the causality and quantify the effects of the drivers"
Phage-Encoded Auxiliary Metabolic Genes for PHA Synthesis Are Transcribed
Seven putative phage-encoded auxiliary metabolic genes potentially contributing to PHA synthesis (phaC, fadJ, acs, ackA, phbB, acdAB, and fadD) were identified by sequence analysis. Metatranscriptomic reads support transcription. Neither the annotations nor the transcripts establish productive lytic infection or increased PHA synthesis yield.
Metabolites: polyhydroxyalkanoate (CHEBI:78037 · MediaIngredientMech · CMMMech)
Biological Processes:
- viral process (GO:0016032 · PathwayMech)
Evidence
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PMID:40152616 - SUPPORT (COMPUTATIONAL)"Seven key auxiliary metabolic genes (AMGs), phaC, fadJ, acs, ackA, phbB, acdAB, and fadD, potentially contributing to PHA synthesis were identified from phage sequences"
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PMID:40152616 - SUPPORT (IN_VITRO)"these AMGs were transcribed, indicating that they were in an active expression state"
Predicted Host Antiviral Defence Repertoire
DefenseFinder predicts encoded antiviral systems in bacterial MAGs: restriction-modification and CRISPR-Cas predominate in 10 of 12 phyla, Wadjet in Actinobacteriota and SoFIC in Planctomycetota; AbiE and Thoeris are also represented. These are sequence-based defense predictions, not functional resistance assays or lytic infections.
Evidence
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PMID:40152616 - SUPPORT (COMPUTATIONAL)"The RM and CRISPR-Cas systems were the predominant antiviral systems in 10 of the 12 bacterial phyla"
Knowledge gaps & discussions (4)
CURATION_TODO OPEN Should the per-reactor, per-timepoint phage-host linkages (for example Brevundimonas with phage 1010E_19 in Reactor A, or the intermittent Paracoccus linkages in Reactor D) be curated as individual LYTIC_INFECTION edges, given that the pOTUs have no stable public identifiers?
The paper reports named phage-host linkages per reactor and per time point in supplementary network figures, and they are the most mechanistically specific content it carries. They are not curated here for two reasons: the phage identifiers (0111B24, 1010E_19) are study-local contig labels with no NCBITaxon or other resolvable grounding, and each linkage holds at some time points and not others, which the schema has no way to qualify. Curating them as unqualified pairwise edges would assert a stability the source explicitly denies. The host links were inferred by CRISPR-spacer matching and sequence homology. Even a resolved study-local identifier would not turn a predicted link into a demonstrated lytic infection.
Attaches to: ecological_interactions#Coupled Turnover of Phage and Bacterial Community Structure
CURATION_TODO OPEN Is a FunctionalRoleEnum value needed for storage-polymer accumulation, which is the defining function of this community and of PHA-MMCs generally?
Every member here is carried with no `functional_role`. The defining function of these genera is accumulating polyhydroxyalkanoate under alternating feast and famine, and no existing value says that. PRIMARY_DEGRADER was considered and rejected: it means degrading complex substrates, while these organisms grow on single short-chain fatty acids and lactate, so using it would assert a metabolism the source does not report — the same failure the PATHOGEN_ANTAGONIST description records for #298/#301. Leaving the slot empty is correct until a value exists, but it does mean the community's central function is readable only from prose and interactions.
Attaches to: taxonomy
OPEN_QUESTION OPEN Should five reactors differing in carbon source and in dominant genus be one record or five?
The five reactors share an inoculum, a selection strategy, and an operating regime, and the paper analyses them as one system, so they are curated as one community. But the dominant genus differs between them — Azoarcus in A and B, Thauera in E — so the DOMINANT rank carried by all five genera here means "dominant in at least one reactor", not "dominant in the community". A reader taking the five dominants as co-dominant in a single vessel would be misled. Splitting per reactor would fix that and lose the cross-reactor comparison that is the paper's design.
Attaches to: taxonomy
KNOWLEDGE_GAP OPEN What direct perturbation or host-lysis measurements would establish phage-mediated succession in these PHA enrichments?
PMID:40152616 reports observational meta-omics and fitted statistical relationships. The kill-the-winner hypothesis and the negative abundance-diversity association are not independent measured causal steps. No downstream arrow is asserted between them. A matched phage addition/removal or host-lysis experiment in these reactors would resolve the causal direction.
Attaches to: ecological_interactions#Hypothesized Kill-the-Winner Succession of Dominant PHA Producers, ecological_interactions#Modeled Association of Phage Abundance with Bacterial Diversity and Activity
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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Primary publication for the PHA-MMC phage succession community
PubMed record for Yao et al. 2025, mSystems, "Phages-bacteria interactions underlying the dynamics of polyhydroxyalkanoate-producing mixed microbial cultures via meta-omics study". |
OTHER | PMID:40152616 |
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DOI landing page
DOI link to the mSystems paper. |
OTHER | doi:10.1128/msystems.00200-25 |
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Temperature | 26 | degree Celsius |
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| Carbon source | acetate, propionate, butyrate, valerate, or lactate (one per reactor) | N/A |
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| Aerobic dynamic feeding cycle | 12 h cycle; feed 10 min, aeration 650 min, settle 50 min, discharge 10 min | N/A |
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| Operating duration | 145 days | N/A |
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Growth Media
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