CoChat
Sign Up
PreprintCited by 6Bacterial biofilms and quorum sensingMicrobial Community Ecology and PhysiologyMethane Hydrates and Related Phenomena

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Diverse quorum sensing systems regulate microbial communication and biogeochemical processes in deep-sea cold seeps

Open access
Peng, Jiaxue, Liu, Xinyue, Wang, Jieni, Meng, Nan, Cai, Runlin, Peng, Yongyi, Han, Yingchun, Liao, Jing, Li, Chengcheng, Rubin-Blum, Maxim, Ma, Qiao, Dong, Xiyang·2024·Microbiome
DOI 10.1101/2024.11.15.623595PMC PMC12781772

Preprint — published as 10.1186/s40168-025-02280-x · Paper page

Open this paper in CoChat — free account

Abstract

Quorum sensing is a fundamental chemical communication mechanism that enables microorganisms to coordinate behavior and adapt to environmental conditions. In deep-sea cold seep ecosystems, where diverse microbial communities thrive, quorum sensing is likely a key mechanism driving microbial interactions. However, the distribution, mechanisms, and ecological roles of quorum sensing in cold seeps remain poorly understood. To address this, we analyzed 173 metagenomes, 33 metatranscriptomes, and 18 metabolomes from 17 global cold seep sites. We identified 299,355 quorum sensing genes from the seep non-redundant gene catalog, representing 34 gene types across six quorum sensing systems, with distribution patterns influenced by sediment depth and seep type. These quorum sensing genes were present in 3,576 metagenome-assembled genomes from 12 archaeal and 108 bacterial phyla, revealing a complex network of intraspecies and interspecies communication. Microbial groups involved in key metabolic processes, such as sulfate-reducing bacteria, anaerobic methanotrophic archaea, diazotrophs and organohalide reducers, were extensively regulated by quorum sensing, influencing biogeochemical cycles of carbon, nitrogen, and sulfur. Phylogenetic analysis and protein domain identification highlighted the functional roles of key quorum sensing-related proteins (e.g., PDEs, CahR, RpfC/G and LuxR) in modulating microbial behaviors, such as motility and chemotaxis. Heterologous expression and metabolomic profiling further confirmed the activity of representative LuxI-R pairs and identified inhibitors of quorum sensing in cold seep sediments. Overall, these findings highlight complexity and significance of quorum sensing in microbial interactions, ecological adaptation, and biogeochemical cycling within cold seep ecosystems, advancing our understanding of microbial communication in the deep biosphere.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/2024.11.15.623595

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 117

  1. 10.1016/j.tim.2024.01.002 · DOI
  2. 10.3390/jmse11081586 · DOI
  3. 10.1038/nrmicro.2016.89 · DOI · Paper page
  4. 10.1038/s41579-019-0186-5 · DOI
  5. 10.1128/mbio.00638-00619 · DOI
  6. 10.1080/09168451.2018.1433992 · DOI
  7. 10.15190/d.2019.13 · DOI
  8. 10.1038/s41467-021-22649-4 · DOI
  9. 10.1038/ismej.2008.13 · DOI
  10. 10.1080/08927010902853516 · DOI
  11. 10.1038/s41467-020-19243-5 · DOI
  12. 10.1016/j.tim.2022.07.006 · DOI
  13. 10.3389/fcimb.2019.00033 · DOI
  14. 10.1038/nrmicro.2016.190 · DOI
  15. 10.1016/j.tim.2010.03.004 · DOI
  16. 10.1002/anie.202314469 · DOI
  17. 10.1038/nature24624 · DOI
  18. 10.1146/annurev-marine-010816-060656 · DOI
  19. 10.3389/fmars.2022.834337 · DOI
  20. 10.1016/j.micres.2022.127102 · DOI
  21. 10.1016/j.mib.2006.10.001 · DOI
  22. 10.1371/journal.pone.0016943 · DOI
  23. 10.1099/mic.0.083956-0 · DOI
  24. 10.1038/ngeo1926 · DOI
  25. 10.1038/s41467-020-19648-2 · DOI
  26. 10.1146/annurev-earth-063016-020052 · DOI
  27. 10.1038/s41467-019-09747-0 · DOI
  28. 10.1146/annurev-micro-041020-024935 · DOI
  29. 10.1038/s41467-023-36877-3 · DOI
  30. 2021, Tracking microbial evolution in the subseafloor biosphere, mSystems, 6, e0073121
  31. 10.1016/j.watres.2023.119814 · DOI
  32. Han, Y. et al. A comprehensive genomic catalog from global cold seeps. Scientific Data 10, 596 (2023). · DOI
  33. 10.1016/j.watres.2018.02.054 · DOI
  34. 10.1073/pnas.1102923108 · DOI
  35. 10.1128/jb.00105-00117 · DOI
  36. 2023, Metagenomic analysis reveals indole signaling effect on microbial community in sequencing batch reactors: Quorum sensing inhibition and antibiotic resistance enrichment, Environmental Research, 229, 115897, 10.1016/j.envres.2023.115897 · DOI
  37. 10.1073/pnas.1919139117 · DOI
  38. 10.1073/pnas.1213344109 · DOI
  39. 10.1186/s40168-022-01367-z · DOI
  40. 10.3389/fmicb.2017.00798 · DOI
  41. 10.2174/1389450120666181123123333 · DOI
  42. Yin, F. et al. Diversity of bacteria with quorum sensing and quenching activities from hydrothermal vents in the Okinawa Trough. Microorganisms 11, 748 (2023). · DOI
  43. 10.1007/s00705-018-3845-3 · DOI
  44. 10.1128/AAC.47.12.3881-3889.2003 · DOI
  45. 10.1038/nbt814 · DOI · Paper page
  46. 10.1038/ismej.2013.240 · DOI
  47. 10.1038/nrmicro1146 · DOI
  48. 10.1016/j.tim.2019.12.004 · DOI
  49. 10.1128/JB.184.23.6472-6480.2002 · DOI
  50. 10.1038/ismej.2014.208 · DOI
  51. 10.1038/s41522-023-00382-8 · DOI
  52. 10.1038/s41467-022-32503-w · DOI
  53. Han, Y. et al. Phylogenetically and structurally diverse reductive dehalogenases link biogeochemical cycles in deep-sea cold seeps. Preprint at https://www.biorxiv.org/content/10.1101/2024.01.23.576788v1 (2024). · DOI
  54. 10.3389/fmicb.2019.00188 · DOI
  55. 10.1021/acs.chemrev.6b00571 · DOI
  56. 10.1093/nar/gkh908 · DOI
  57. 10.1016/j.csbj.2021.06.020 · DOI
  58. 10.1128/JB.184.21.5946-5954.2002 · DOI
  59. 10.1038/nrmicro2203 · DOI
  60. 10.1146/annurev.genet.40.110405.090423 · DOI
  61. 10.1038/s41564-023-01468-x · DOI
  62. 10.1007/s00018-017-2514-0 · DOI
  63. 10.1111/j.1472-765X.2008.02460.x · DOI
  64. 10.1002/pro.2237 · DOI
  65. 10.1128/jb.184.4.1204-1208.2002 · DOI
  66. 10.1046/j.1365-2958.2000.02196.x · DOI
  67. 10.1111/j.1365-2958.2005.04961.x · DOI
  68. 10.1111/j.1365-2958.2007.05670.x · DOI
  69. 10.1128/JB.01253-09 · DOI
  70. 10.1146/annurev.micro.55.1.165 · DOI
  71. 10.1016/j.biortech.2022.127394 · DOI
  72. 10.1093/femsle/fnad055 · DOI
  73. Jiang, Q. et al. Cold seeps are hotspots of deep-sea nitrogen-loss driven by microorganisms across 21 phyla. Preprint at https://www.biorxiv.org/content/10.1101/2024.06.05.597523v1 (2024). · DOI
  74. 2024, SoxY gene family expansion underpins adaptation to diverse hosts and environments in symbiotic sulfide oxidizers, mSystems, 9, e01135
  75. 10.1016/j.gca.2024.04.003 · DOI
  76. 10.1089/fpd.2008.0106 · DOI
  77. 2018, Environmental adaptability and quorum sensing: iron uptake regulation during biofilm formation by Paracoccus denitrificans, Applied and Environmental Microbiology, 84, e00865
  78. 10.1038/ncomms6945 · DOI
  79. 2019, Designing quorum sensing inhibitors of Pseudomonas aeruginosa utilizing FabI: an enzymic drug target from fatty acid synthesis pathway, 3 Biotech, 9, 1
  80. 10.1002/mlf2.12144 · DOI
  81. Senthil, R. , Archunan, G. , Vithya, D. & Saravanan, K. M . Hexadecanoic acid analogs as potential CviR-mediated quorum sensing inhibitors in Chromobacterium violaceum: an in silico study. Journal of Biomolecular Structure and Dynamics, 1–10 (2023). · DOI
  82. 10.3390/biomedicines9091133 · DOI · Paper page
  83. 10.1111/j.1750-3841.2007.00527.x · DOI
  84. 10.1128/mbio.01054-01016 · DOI
  85. Han, Y. et al. Diverse defense systems synergistically drive the microbe-virus arms race in deep sea cold seeps. Preprint at https://www.biorxiv.org/content/10.1101/2024.09.26.614923v1 (2024). · DOI · Paper page
  86. 10.1093/bioinformatics/btv033 · DOI
  87. 10.1186/1471-2105-11-1 · DOI
  88. 10.1093/bioinformatics/bts565 · DOI · Paper page
  89. 10.1038/nmeth.4197 · DOI · Paper page
  90. 10.1038/ismej.2017.126 · DOI · Paper page
  91. 10.1093/nar/gkab776 · DOI · Paper page
  92. 10.1093/molbev/msp077 · DOI · Paper page
  93. 10.1093/NAR/GKAB301 · DOI
  94. 10.1093/BIOINFORMATICS/BTZ715 · DOI
  95. 10.1093/nar/gkaa621 · DOI
  96. 10.1186/s40168-018-0420-9 · DOI
  97. 10.1093/bioinformatics/bts611 · DOI
  98. 10.1093/bioinformatics/bty121 · DOI
  99. 10.1093/bioinformatics/btp348 · DOI
  100. 10.1093/bioinformatics/btp033 · DOI
  101. 10.1093/nar/gku949 · DOI
  102. 10.1038/s41587-023-01773-0 · DOI · Paper page
  103. 10.1093/bioinformatics/btq066 · DOI · Paper page
  104. 2002, Pymol: An open-source molecular graphics tool, CCP4 Newsl. Protein Crystallogr, 40, 82
  105. Camargo, A. P. et al. Identification of mobile genetic elements with geNomad. Nature Biotechnology, 1–10 (2023). · DOI
  106. 10.1038/s41587-020-00774-7PMID-33349699 · DOI
  107. 10.1101/gr.1239303 · DOI · Paper page
  108. 10.1609/icwsm.v3i1.13937 · DOI · Paper page
  109. 10.1186/s40168-021-01213-8 · DOI
  110. 2021, DiSCo: a sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur metabolism in microbial data, Microbial Genomics, 7, 000603
  111. 10.1038/s41592-021-01101-x · DOI · Paper page
  112. 10.1093/bioinformatics/bty741 · DOI
  113. 10.1039/C9EM00605B · DOI
  114. 10.1093/nar/gkv416 · DOI
  115. 10.1038/s41522-021-00250-3 · DOI
  116. 10.1016/j.chemosphere.2019.02.192 · DOI
  117. 10.1007/s11104-020-04630-0 · DOI

Metadata

Authors
Peng, J., Liu, X., Wang, J., Meng, N., Cai, R., Peng, Y., Han, Y., Liao, J., Li, C., Rubin-Blum, M., Ma, Q., & Dong, X.
Affiliations
  • Ministry of Natural Resources (CN)
  • Dalian Maritime University (CN)
  • Shantou University (CN)
  • Chinese Academy of Sciences (CN)
Corresponding author
  • Ma, Qiao
  • Dong, Xiyang
ORCID
Venue
Microbiome
Publisher
openRxiv
Published
2024-11-16
Volume
14
Issue
1
Pages
16-16
ISSN
2049-2618 (ISSN-L)
DOI
10.1101/2024.11.15.623595
PMC
PMC12781772
OpenAlex
W4416936604
Cited by
6
References
1
Citations by year
2026: 6
FWCI
1.79
Type
journal article
Language
en
Open access
Licence
Locations
  • Microbiome (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • National Natural Science Foundation of China (32170121, 92351304)
  • Natural Science Foundation of Fujian Province (2023J06042)
  • Israel Science Foundation (1359/23)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bacterial biofilms and quorum sensing
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
  • Physical Sciences › Environmental Science › Environmental Chemistry › Methane Hydrates and Related Phenomena
Keywords
quorum sensing, deep-sea cold seeps, microbial communication, quorum sensing genes, metagenome-assembled genomes, sulfate-reducing bacteria, anaerobic methanotrophic archaea, nitrogen-fixing bacteria, biogeochemical cycles, quorum sensing inhibitors, chemotaxis, deep biosphere, metatranscriptomics
MeSH terms
Archaea, Bacteria, Phylogeny, Seawater, Ecosystem, Geologic Sediments, Quorum Sensing, Metagenome, Microbiota

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review