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Add propanotrophic chlorinated-ethene cometabolism community (#73)
* Add propanotrophic chlorinated-ethene cometabolism community Curate a new community YAML (CommunityMech:000271) from Faghihinezhad, Eshghdoostkhatami, Cupples 2026 Journal of Environmental Management, doi:10.1016/j.jenvman.2026.129957, "Characterization of multiple trichloroethene, cis-dichloroethene and 1,1-dichloroethene degrading propanotrophic communities". System: propane-enriched aerobic mixed cultures derived from three KBS-LTER agricultural soils (T2, T3, T4) and an impacted-site sediment (West Coast Naval Station, Site 1), evaluated for cometabolic biodegradation of TCE, cDCE, and 1,1-DCE over successive transfers. Members and roles: - Rhodococcus opacus and R. wratislaviensis (PRIMARY_DEGRADER, DOMINANT in TCE-amended enrichments) - Mycolicibacterium and Mycobacterium (PRIMARY_DEGRADER, dominant in cDCE-amended enrichments) - Pseudonocardia (PRIMARY_DEGRADER, dominant in 1,1-DCE-degrading cultures; carries truncated prmA so transformation enzyme unclear - PARTIAL) - Pseudonocardia broussonetiae (Site-1-specific MAG) - Methylibium and an unclassified Burkholderiaceae (CROSS_FEEDER, RARE non-actinobacterial propane-monooxygenase MAGs from cDCE enrichments) Interactions captured: - Propane-cometabolic TCE degradation by Rhodococcus (CROSS_FEEDING via group-5 prmABCD) - Propane-cometabolic cDCE degradation by Mycolicibacterium and Mycobacterium (CROSS_FEEDING via group-6 SDIMO with prmACDB ordering - PARTIAL since expression not examined) - Substrate-specific selection across the three chlorinated ethenes (COMPETITION at COMMUNITY_LEVEL) - 1,1-DCE-driven inhibition of propanotrophs (COMPETITION at COMMUNITY_LEVEL) Plus four environmental factors: propane growth substrate, chlorinated-ethene concentration ranges, inoculum source, aerobic shaken incubation. Storage: - Full-text PDF tracked at references_pdfs/Faghihinezhad_2026_propanotrophic_TCE_cDCE_DCE.pdf (new directory; no prior PDF storage convention in the repo). - references_cache/DOI_10.1016_j.jenvman.2026.129957.md now carries the full-text extracted from the PDF (content_type: full_text), enabling snippet validation against methods/results passages that the abstract alone does not cover. All snippets validate as substrings of the cached full text; `just validate-references-all` reports 39 errors (unchanged from main - the new community adds zero). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * Address Copilot review on PR #73 Six review points from Copilot: - Cache cleanup: re-extract the PDF text with control-byte removal and paragraph-aware wrapping. The previous version of the cache contained 6 NUL bytes + 6 other ASCII control bytes (which could flip the file to binary in some tools) and was stored as a single ~109 kB line. Now: 0 NUL/control bytes, sentence-respecting paragraph layout wrapped at 100 columns, same content, all snippets still validate. - CHEBI ID for trichloroethene: 18045 -> 16602 to match the repo- standard term used by 4 other chlorinated-ethene communities (Dehalococcoides Syntrophomonas / Pelobacter / Desulfovibrio cocultures and KB1). - Mycolicibacterium notes: drop the unsourced claim that this genus carries prmACDB-ordered group-6 SDIMO operons. The paper's MAG-level results report propane monooxygenase operons on Rhodococcus, Mycobacterium, and Pseudonocardia MAGs, plus two Proteobacterial MAGs; the prmACDB ordering is specifically attributed to Mycobacterium. Updated notes flag that Mycolicibacterium dominance is from community-composition analysis, not MAG-level prm operons. - TCE-cometabolism description softened: the previous wording "the group-5 propane monooxygenase (prmABCD) is implicated as the enzyme that fortuitously oxidizes TCE" is stronger than the abstract supports (functional gene analysis identified the operons but expression was not examined). Now: states that Rhodococcus MAGs carry the prmABCD operon and that both group 5 and putative group 6 monooxygenases were identified in the community, with the caveat that expression was not examined and the in-vivo TCE-oxidizing enzyme is not directly demonstrated. - 1,1-DCE-inhibition description softened: drop the unsupported "rather than its irreversible transformation products" assertion. The evidence supports inhibitory/toxic effects at elevated concentrations but does not distinguish parent compound vs. transformation products; description now reflects that limitation explicitly. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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‎kb/communities/Propanotrophic_Chlorinated_Ethene_Cometabolism_Enrichment.yaml‎

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‎references_cache/DOI_10.1016_j.algal.2016.05.024.md‎

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---
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reference_id: DOI:10.1016/j.algal.2016.05.024
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title: "Cofactor symbiosis for enhanced algal growth, biofuel production, and wastewater treatment"
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authors:
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- Brendan T. Higgins
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- Ingrid Gennity
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- Stephanie Samra
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- Tobias Kind
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- Oliver Fiehn
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- Jean S. VanderGheynst
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journal: Algal Research
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year: '2016'
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doi: 10.1016/j.algal.2016.05.024
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content_type: unavailable
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---
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# Cofactor symbiosis for enhanced algal growth, biofuel production, and wastewater treatment
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**Authors:** Brendan T. Higgins, Ingrid Gennity, Stephanie Samra, Tobias Kind, Oliver Fiehn, Jean S. VanderGheynst
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**Journal:** Algal Research (2016)
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**DOI:** [10.1016/j.algal.2016.05.024](https://doi.org/10.1016/j.algal.2016.05.024)
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## Content

‎references_cache/DOI_10.1016_j.ijhydene.2015.05.135.md‎

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reference_id: DOI:10.1016/j.ijhydene.2015.05.135
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title: Effects of cellulose concentrations on the syntrophic interactions between Clostridium cellulovorans 743B and Rhodopseudomonas palustris CGA009 in coculture fermentation for biohydrogen production
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authors:
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- Hongyuan Lu
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- Patrick K.H. Lee
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journal: International Journal of Hydrogen Energy
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year: '2015'
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doi: 10.1016/j.ijhydene.2015.05.135
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content_type: unavailable
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---
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# Effects of cellulose concentrations on the syntrophic interactions between Clostridium cellulovorans 743B and Rhodopseudomonas palustris CGA009 in coculture fermentation for biohydrogen production
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**Authors:** Hongyuan Lu, Patrick K.H. Lee
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**Journal:** International Journal of Hydrogen Energy (2015)
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**DOI:** [10.1016/j.ijhydene.2015.05.135](https://doi.org/10.1016/j.ijhydene.2015.05.135)
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## Content

‎references_cache/DOI_10.1016_j.jenvman.2026.129957.md‎

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‎references_cache/DOI_10.1126_science.aaa4834.md‎

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---
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reference_id: DOI:10.1126/science.aaa4834
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title: Redox cycling of Fe(II) and Fe(III) in magnetite by Fe-metabolizing bacteria
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authors:
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- James M. Byrne
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- Nicole Klueglein
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- Carolyn Pearce
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- Kevin M. Rosso
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- Erwin Appel
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- Andreas Kappler
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journal: Science
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year: '2015'
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doi: 10.1126/science.aaa4834
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content_type: abstract_only
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---
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# Redox cycling of Fe(II) and Fe(III) in magnetite by Fe-metabolizing bacteria
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**Authors:** James M. Byrne, Nicole Klueglein, Carolyn Pearce, Kevin M. Rosso, Erwin Appel, Andreas Kappler
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**Journal:** Science (2015)
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**DOI:** [10.1126/science.aaa4834](https://doi.org/10.1126/science.aaa4834)
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## Content
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Building a biogeochemical battery
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Iron acts as both a source and sink of electrons for microorganisms in the environment. Some anaerobic bacteria use oxidized Fe(III) as an electron acceptor, whereas phototrophic bacteria can use reduced Fe(II) as an electron donor. Byrne
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et al.
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show that the iron-bearing mineral magnetite, which contains both Fe(II) and Fe(III), can serve as both an electron acceptor and donor. Cocultures of iron-reducing and iron-oxidizing bacteria exposed to simulated day/night cycles or changes in organic matter altered the ratio of Fe(II) to Fe(III) in magnetite particles.
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Science
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, this issue p.
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1473

‎references_cache/DOI_10.1128_AEM.00789-16.md‎

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reference_id: DOI:10.1128/AEM.00789-16
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title: Transcriptomic Responses of the Interactions between Clostridium cellulovorans 743B and Rhodopseudomonas palustris CGA009 in a Cellulose-Grown Coculture for Enhanced Hydrogen Production
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authors:
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- Hongyuan Lu
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- Jiahua Chen
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- Yangyang Jia
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- Mingwei Cai
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- Patrick K. H. Lee
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journal: Applied and Environmental Microbiology
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year: '2016'
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doi: 10.1128/AEM.00789-16
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content_type: abstract_only
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---
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# Transcriptomic Responses of the Interactions between Clostridium cellulovorans 743B and Rhodopseudomonas palustris CGA009 in a Cellulose-Grown Coculture for Enhanced Hydrogen Production
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**Authors:** Hongyuan Lu, Jiahua Chen, Yangyang Jia, Mingwei Cai, Patrick K. H. Lee
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**Journal:** Applied and Environmental Microbiology (2016)
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**DOI:** [10.1128/AEM.00789-16](https://doi.org/10.1128/AEM.00789-16)
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## Content
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ABSTRACT
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Coculturing dark- and photofermentative bacteria is a promising strategy for enhanced hydrogen (H
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2
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) production. In this study, next-generation sequencing was used to query the global transcriptomic responses of an artificial coculture of
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Clostridium cellulovorans
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743B and
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Rhodopseudomonas palustris
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CGA009. By analyzing differentially regulated gene expression, we showed that, consistent with the physiological observations of enhanced H
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2
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production and cellulose degradation, the nitrogen fixation genes in
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R. palustris
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and the cellulosomal genes in
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C. cellulovorans
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were upregulated in cocultures. Unexpectedly, genes related to H
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2
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production in
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C. cellulovorans
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were downregulated, suggesting that the enhanced H
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2
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yield was contributed mainly by
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R. palustris
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. A number of genes related to biosynthesis of volatile fatty acids (VFAs) in
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C. cellulovorans
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were upregulated, and correspondingly, a gene that mediates organic compound catabolism in
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R. palustris
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was also upregulated. Interestingly, a number of genes responsible for chemotaxis in
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R. palustris
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were upregulated, which might be elicited by the VFA concentration gradient created by
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C. cellulovorans
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. In addition, genes responsible for sulfur and thiamine metabolism in
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C. cellulovorans
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were downregulated in cocultures, and this could be due to a response to pH changes. A conceptual model illustrating the interactions between the two organisms was constructed based on the transcriptomic results.
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IMPORTANCE
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The findings of this study have important biotechnology applications for biohydrogen production using renewable cellulose, which is an industrially and economically important bioenergy process. Since the molecular characteristics of the interactions of a coculture when cellulose is the substrate are still unclear, this work will be of interest to microbiologists seeking to better understand and optimize hydrogen-producing coculture systems.

‎references_cache/PMID_16346269.md‎

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---
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reference_id: PMID:16346269
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title: Photoproduction of h(2) from cellulose by an anaerobic bacterial coculture.
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authors:
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- Odom JM
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- Wall JD
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journal: Appl Environ Microbiol
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year: '1983'
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doi: 10.1128/aem.45.4.1300-1305.1983
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content_type: abstract_only
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---
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# Photoproduction of h(2) from cellulose by an anaerobic bacterial coculture.
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**Authors:** Odom JM, Wall JD
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**Journal:** Appl Environ Microbiol (1983)
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**DOI:** [10.1128/aem.45.4.1300-1305.1983](https://doi.org/10.1128/aem.45.4.1300-1305.1983)
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## Content
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1. Appl Environ Microbiol. 1983 Apr;45(4):1300-5. doi:
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10.1128/aem.45.4.1300-1305.1983.
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Photoproduction of h(2) from cellulose by an anaerobic bacterial coculture.
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Odom JM(1), Wall JD.
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Author information:
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(1)Biochemistry Department, University of Missouri, Columbia, Missouri 65211.
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Cellulomonas sp. strain ATCC 21399 is a facultatively anaerobic,
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cellulose-degrading microorganism that does not evolve hydrogen but produces
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organic acids during cellulose fermentation. Rhodopseudomonas capsulata cannot
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utilize cellulose, but grows photoheterotrophically under anaerobic conditions
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on organic acids or sugars. This report describes an anaerobic coculture of the
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Cellulomonas strain with wild-type R. capsulata or a mutant strain lacking
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uptake hydrogenase, which photoevolves molecular hydrogen by the nitrogenase
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system of R. capsulata with cellulose as the sole carbon source. In coculture,
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the hydrogenase-negative mutant produced 4.6 to 6.2 mol of H(2) per mol of
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glucose equivalent, compared with 1.2 to 4.3 mol for the wild type.
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DOI: 10.1128/aem.45.4.1300-1305.1983
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PMCID: PMC242454
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PMID: 16346269

‎references_cache/PMID_24805253.md‎

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---
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reference_id: PMID:24805253
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title: Effects of Escherichia coli on mixotrophic growth of Chlorella minutissima and production of biofuel precursors.
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authors:
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- Higgins BT
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- VanderGheynst JS
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journal: PLoS One
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year: '2014'
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doi: 10.1371/journal.pone.0096807
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keywords:
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- Biofuels/microbiology
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- Biomass
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- Carbon/metabolism
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- "Chlorella/genetics, growth & development, metabolism"
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- Coculture Techniques
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- Culture Media
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- "Escherichia coli/genetics, growth & development, metabolism"
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- Glucose/biosynthesis
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- Humans
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- Starch/biosynthesis
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content_type: abstract_only
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---
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# Effects of Escherichia coli on mixotrophic growth of Chlorella minutissima and production of biofuel precursors.
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**Authors:** Higgins BT, VanderGheynst JS
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**Journal:** PLoS One (2014)
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**DOI:** [10.1371/journal.pone.0096807](https://doi.org/10.1371/journal.pone.0096807)
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## Content
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1. PLoS One. 2014 May 7;9(5):e96807. doi: 10.1371/journal.pone.0096807.
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eCollection 2014.
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Effects of Escherichia coli on mixotrophic growth of Chlorella minutissima and
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production of biofuel precursors.
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Higgins BT(1), VanderGheynst JS(1).
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Author information:
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(1)Biological and Agricultural Engineering, University of California Davis,
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Davis, California, United States of America.
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Chlorella minutissima was co-cultured with Escherichia coli in airlift reactors
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under mixotrophic conditions (glucose, glycerol, and acetate substrates) to
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determine possible effects of bacterial contamination on algal biofuel
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production. It was hypothesized that E. coli would compete with C. minutissima
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for nutrients, displacing algal biomass. However, C. minutissima grew more
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rapidly and to higher densities in the presence of E. coli, suggesting a
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symbiotic relationship between the organisms. At an initial 1% substrate
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concentration, the co-culture produced 200-587% more algal biomass than the
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axenic C. minutissima cultures. Co-cultures grown on 1% substrate consumed
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23-737% more of the available carbon substrate than the sum of substrate
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consumed by E. coli and C. minutissima alone. At 1% substrate, total lipid and
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starch productivity were elevated in co-cultures compared to axenic cultures
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indicating that bacterial contamination was not detrimental to the production of
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biofuel precursors in this specific case. Bio-fouling of the reactors observed
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in co-cultures and acid formation in all mixotrophic cultures, however, could
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present challenges for scale-up.
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DOI: 10.1371/journal.pone.0096807
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PMCID: PMC4013066
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PMID: 24805253 [Indexed for MEDLINE]
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Conflict of interest statement: Competing Interests: The authors have declared
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that no competing interests exist.

‎references_cache/PMID_25814583.md‎

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---
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reference_id: PMID:25814583
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title: Redox cycling of Fe(II) and Fe(III) in magnetite by Fe-metabolizing bacteria.
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authors:
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- Byrne JM
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- Klueglein N
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- Pearce C
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- Rosso KM
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- Appel E
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- Kappler A
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journal: Science
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year: '2015'
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doi: 10.1126/science.aaa4834
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keywords:
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- Coculture Techniques
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- Electrons
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- Ferrosoferric Oxide/metabolism
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- "Geobacter/growth & development, metabolism"
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- Iron/metabolism
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- Light
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- Magnetite Nanoparticles
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- Oxidation-Reduction
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- "Rhodopseudomonas/growth & development, metabolism"
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content_type: abstract_only
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---
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# Redox cycling of Fe(II) and Fe(III) in magnetite by Fe-metabolizing bacteria.
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**Authors:** Byrne JM, Klueglein N, Pearce C, Rosso KM, Appel E, Kappler A
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**Journal:** Science (2015)
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**DOI:** [10.1126/science.aaa4834](https://doi.org/10.1126/science.aaa4834)
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## Content
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1. Science. 2015 Mar 27;347(6229):1473-6. doi: 10.1126/science.aaa4834.
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Redox cycling of Fe(II) and Fe(III) in magnetite by Fe-metabolizing bacteria.
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Byrne JM(1), Klueglein N(2), Pearce C(3), Rosso KM(4), Appel E(5), Kappler A(2).
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Author information:
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(1)Geomicrobiology, Center for Applied Geosciences, University of Tuebingen,
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Sigwartstrasse 10, 72076 Tuebingen, Germany. James.Byrne@uni-tuebingen.de.
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(2)Geomicrobiology, Center for Applied Geosciences, University of Tuebingen,
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Sigwartstrasse 10, 72076 Tuebingen, Germany.
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(3)School of Chemistry, University of Manchester, M13 9PL Manchester, UK.
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Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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(4)Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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(5)Geophysics, Center for Applied Geosciences, University of Tuebingen,
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Sigwartstrasse 10, 72076 Tuebingen, Germany.
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Microorganisms are a primary control on the redox-induced cycling of iron in the
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environment. Despite the ability of bacteria to grow using both Fe(II) and
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Fe(III) bound in solid-phase iron minerals, it is currently unknown whether
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changing environmental conditions enable the sharing of electrons in
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mixed-valent iron oxides between bacteria with different metabolisms. We show
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through magnetic and spectroscopic measurements that the phototrophic
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Fe(II)-oxidizing bacterium Rhodopseudomonas palustris TIE-1 oxidizes magnetite
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(Fe3O4) nanoparticles using light energy. This process is reversible in
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co-cultures by the anaerobic Fe(III)-reducing bacterium Geobacter
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sulfurreducens. These results demonstrate that Fe ions bound in the highly
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crystalline mineral magnetite are bioavailable as electron sinks and electron
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sources under varying environmental conditions, effectively rendering magnetite
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a naturally occurring battery.
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Copyright © 2015, American Association for the Advancement of Science.
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DOI: 10.1126/science.aaa4834
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PMID: 25814583 [Indexed for MEDLINE]

‎references_cache/PMID_34669248.md‎

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---
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reference_id: PMID:34669248
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title: Synthetic co-culture of autotrophic Clostridium carboxidivorans and chain elongating Clostridium kluyveri monitored by flow cytometry.
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authors:
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- Bäumler M
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- Schneider M
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- Ehrenreich A
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- Liebl W
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- Weuster-Botz D
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journal: Microb Biotechnol
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year: '2022'
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doi: 10.1111/1751-7915.13941
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keywords:
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- 1-Butanol
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- Bioreactors/microbiology
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- Butanols
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- Clostridium
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- Clostridium kluyveri
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- Coculture Techniques
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- Ethanol
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- Fermentation
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- Flow Cytometry
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- Hexanols
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- "In Situ Hybridization, Fluorescence"
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content_type: abstract_only
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---
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# Synthetic co-culture of autotrophic Clostridium carboxidivorans and chain elongating Clostridium kluyveri monitored by flow cytometry.
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**Authors:** Bäumler M, Schneider M, Ehrenreich A, Liebl W, Weuster-Botz D
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**Journal:** Microb Biotechnol (2022)
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**DOI:** [10.1111/1751-7915.13941](https://doi.org/10.1111/1751-7915.13941)
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## Content
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1. Microb Biotechnol. 2022 May;15(5):1471-1485. doi: 10.1111/1751-7915.13941.
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Epub 2021 Oct 20.
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Synthetic co-culture of autotrophic Clostridium carboxidivorans and chain
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elongating Clostridium kluyveri monitored by flow cytometry.
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Bäumler M(1), Schneider M(2), Ehrenreich A(2), Liebl W(2), Weuster-Botz D(1).
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Author information:
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(1)Institute of Biochemical Engineering, TUM School of Engineering and Design,
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Technical University of Munich, Boltzmannstr. 15, Garching, 85748, Germany.
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(2)Chair of Microbiology, TUM School of Life Sciences, Technical University of
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Munich, Emil-Ramann-Str. 4, Freising, Germany.
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Syngas fermentation with acetogens is known to produce mainly acetate and
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ethanol efficiently. Co-cultures with chain elongating bacteria making use of
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these products are a promising approach to produce longer-chain alcohols.
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Synthetic co-cultures with identical initial cell concentrations of Clostridium
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carboxidivorans and Clostridium kluyveri were studied in batch-operated
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stirred-tank bioreactors with continuous CO/CO2 -gassing and monitoring of the
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cell counts of both clostridia by flow cytometry after fluorescence in situ
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hybridization (FISH-FC). At 800 mbar CO, chain elongation activity was observed
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at pH 6.0, although growth of C. kluyveri was restricted. Organic acids produced
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by C. kluyveri were reduced by C. carboxidivorans to the corresponding alcohols
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butanol and hexanol. This resulted in a threefold increase in final butanol
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concentration and enabled hexanol production compared with a mono-culture of C.
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carboxidivorans. At 100 mbar CO, growth of C. kluyveri was improved; however,
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the capacity of C. carboxidivorans to form alcohols was reduced. Because of the
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accumulation of organic acids, a constant decay of C. carboxidivorans was
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observed. The measurement of individual cell concentrations in co-culture
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established in this study may serve as an effective tool for knowledge-based
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identification of optimum process conditions for enhanced formation of
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longer-chain alcohols by clostridial co-cultures.
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© 2021 The Authors. Microbial Biotechnology published by Society for Applied
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Microbiology and John Wiley & Sons Ltd.
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DOI: 10.1111/1751-7915.13941
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PMCID: PMC9049614
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PMID: 34669248 [Indexed for MEDLINE]
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Conflict of interest statement: None declared.

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