Published June 30, 2025 | Version Submitted
Discussion Paper Open

Deep sea anaerobic microbial community couples the degradation of insoluble chitin to extracellular electron transfer

Abstract

Chitin is a major structural component of arthropod exoskeletons, and an important carbon and nitrogen source in marine environments. In anoxic sediments, its degradation generates chitooligosaccharides and N-acetylglucosamine (GlcNAc), which are fermented into smaller organic molecules and oxidized anaerobically using soluble electron acceptors or insoluble ones such as metal oxides. To date, many aspects of chitin degradation in deep-sea anoxic sediments have been overlooked, including the potential coupling of insoluble chitin degradation to metal oxide reduction, the involvement of extracellular electron transfer (EET), and the spatial organization of the microorganisms involved. Using anoxic deep-sea sediments recovered from a whale fall site, we developed an innovative workflow based on electrochemical reactors, to characterize chitin degradation in these environments. Sediment samples enriched on poorly crystalline iron oxides, and subsequently transferred into an electrochemical reactor poised at +0.22 V vs SHE, showed active anodic current production when supplied with chitin, which increased 2-fold when amended with GlcNAc. Chitin reactors were dominated byVallitalea(Firmicutes),Spirochaetota,GammaproteobacteriaandDesulfobacterota. Exoenzyme activity assays, metabolite profiling, and continued anodic current production confirmed ongoing chitin degradation linked to EET. We observed metabolic associations between chitin degraders and secondary consumers usingin situimaging (16S rRNA gene FISH coupled with BONCAT and nanoSIMS). These microbial partners, within the electrode-attached community, required close proximity to the poised electrode (≤ 10 µm) to remain metabolically active. Supporting these observations, cultured isolates ofVallitaleasp. andTrichloromonassp. recovered from the whale fall site exhibited chitin degradation and electrochemical activity, respectively. When co-cultured in an bioelectrochemical reactor, the acetate produced byVallitaleasp. during chitin degradation fueledTrichloromonassp., which facilitated EET, hereby demonstrating that syntrophic interactions are used to couple anoxic chitin degradation to EET in deep-sea sediments. These findings exemplify the interspecies interactions and resource optimization occurring in hard-to-reach and largely unknown deep-sea ecosystems.

Copyright and License

The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.

Acknowledgement

We are grateful to members of the Orphan lab for discussions regarding this work. Dr. Daniel Utter provided critical readings that improved this manuscript. This research was supported by the SIMONS foundation Life Sciences-Simons Collaboration on Principles of Microbial Ecosystems (PriME); Award XXXXXXX). Ship time on the R/V Western Flyer and deep-sea sampling with the ROV Doc Ricketts was made possible by the Monterey Bay Aquarium Research Institute (MBARI) where VJO is an adjunct investigator. We extend our gratitude to Dr.

Nathan Dalleska for training and access to the Resnick Water and Environment Lab (WEL), Dr. Giada Spigolon for guidance with LSM 980 hosted at Beckman Biological Imaging Center, and Dr. Yunbin Guan for his expertise with nanoSIMS operations. We also thank Dr. Doug LaRowe and Dr. Grayson Boyer for insightful discussions on Gibbs free energy calculations. We thank Emmanuelle Botté (Manuscribe) for her support in reviewing and editing this manuscript. VJO is a CIFAR research fellow in the Earth 4D program.

Data Availability

All raw data and analysis code used to generate the figures, extended data, and supplementary materials supporting the statements in this manuscript are available via the Caltech Research Data Repository (Ref: 10.22002/5hw6d-sw55). The raw sequencing data have been uploaded to National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (accession number: XXXXXXX) under BioProject YYYYYYY.

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Additional details

Funding

Simons Foundation

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Caltech groups
Division of Biology and Biological Engineering (BBE), Division of Geological and Planetary Sciences (GPS)
Publication Status
Submitted