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Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle

Nature Microbiology volume 4, pages 864–875 (2019)Cite this article

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Abstract

Beneficial microbial associations enhance the fitness of most living organisms, and wood-feeding insects offer some of the most striking examples of this. Odontotaenius disjunctus is a wood-feeding beetle that possesses a digestive tract with four main compartments, each of which contains well-differentiated microbial populations, suggesting that anatomical properties and separation of these compartments may enhance energy extraction from woody biomass. Here, using integrated chemical analyses, we demonstrate that lignocellulose deconstruction and fermentation occur sequentially across compartments, and that selection for microbial groups and their metabolic pathways is facilitated by gut anatomical features. Metaproteogenomics showed that higher oxygen concentration in the midgut drives lignocellulose depolymerization, while a thicker gut wall in the anterior hindgut reduces oxygen diffusion and favours hydrogen accumulation, facilitating fermentation, homoacetogenesis and nitrogen fixation. We demonstrate that depolymerization continues in the posterior hindgut, and that the beetle excretes an energy- and nutrient-rich product on which its offspring subsist and develop. Our results show that the establishment of beneficial microbial partners within a host requires both the acquisition of the microorganisms and the formation of specific habitats within the host to promote key microbial metabolic functions. Together, gut anatomical properties and microbial functional assembly enable lignocellulose deconstruction and colony subsistence on an extremely nutrient-poor diet.

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Fig. 1: Digestive tract of O. disjunctus.
Fig. 2: Wood biomass is transformed as it passes through the digestive tract of O. disjunctus.
Fig. 3: Distribution of the microbial genetic potential for lignocellulose degradation and its expression through the digestive tract of O. disjunctus.
Fig. 4: Schematic representation of the coverage and expression of microbial metabolic pathway distribution through the beetle gut from the metagenomic and metaproteomic analyses.
Fig. 5: Hydrogen and methane production, as well as nitrogen fixation, occur in the beetle’s digestive tract.
Fig. 6: Distribution of processes for the deconstruction and fermentation of lignocellulose in the digestive tract of O. disjunctus, and key microbial players.

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Data availability

Metagenomic data are publicly available at the National Center for Biotechnology Information under the BioProject PRJNA510434. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD012200. Metabolomics data can be found at https://osf.io/qey67/.

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Acknowledgements

This work was funded by the Department of Energy’s Genomic Science Program (grant SCW1039). Part of this work was performed at Lawrence Berkeley National Laboratory and Lawrence Livermore National Laboratory under United States Department of Energy contract numbers DE-AC02-05CH11231 and DE-AC52-07NA27344, respectively. A portion of this research was also performed under an Environmental Molecular Sciences Laboratory Science Theme Project (awarded to E.L.B.), which is a Department of Energy Office of Science User Facility sponsored by the Office of Biological and Environmental Research and operated under contract DE-AC05-76RL01830 (EMSL). DNA sequencing was performed at the Vincent J. Coates Genomics Sequencing Laboratory at the University of California Berkeley, supported by NIH S10 Instrumentation grants S10RR029668 and S10RR027303. We thank K. Burnum-Johnson for helpful discussion.

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Authors and Affiliations

  1. Ecology Department, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA

    Javier A. Ceja-Navarro, Ulas Karaoz, Markus Bill, Zhao Hao, Abelardo Arellano, Leila Ramanculova, Mark E. Conrad & Eoin L. Brodie

  2. Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA

    Richard A. White III, Carrie D. Nicora & Young-Mo Kim

  3. Department of Earth, Atmospheric, and Planetary Sciences, Purdue University, West Lafayette, IN, USA

    Timothy R. Filley & Timothy D. Berry

  4. Department of Soil Science, University of Wisconsin, Madison, WI, USA

    Timothy D. Berry

  5. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA

    Meredith Blackwell

  6. University of South Carolina, Columbia, SC, USA

    Meredith Blackwell & Joshua N. Adkins

  7. NMR Facility, Oregon State University, Corvallis, OR, USA

    Patrick N. Reardon

  8. Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA

    Mary S. Lipton

  9. Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA

    Jennifer Pett-Ridge

  10. Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA

    Eoin L. Brodie

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Contributions

J.A.C.-N. and E.L.B. designed the experiments and wrote the manuscript. J.A.C.-N. and U.K. performed the bioinformatics and statistical analyses. A.A. and L.R. contributed with bioinformatics analyses. J.A.C.-N. performed the microelectrode work. M.B., J.A.C.-N. and M.E.C. generated the methane dynamics and methane fractionation data. Z.H. generated the infrared data. T.R.F. and T.D.B. generated the thermochemolysis data. J.N.A., M.S.L., R.A.W. and C.D.N. contributed with metaproteomics analyses. Y.-M.K. and R.A.W. generated the GC-MS data. P.N.R. generated the NMR data. M.B. provided the insect specimens and contributed with manuscript preparation. J.P.-R. contributed with manuscript preparation.

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Correspondence to Eoin L. Brodie.

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Supplementary information

Supplementary Information

Supplementary Figures 1–5, Supplementary Tables 1–3 and legends for Supplementary Datasets.

Reporting Summary

Supplementary Dataset 1

Fasta file containing all metagenome-assembled contigs.

Supplementary Dataset 2

Fasta file containing all the metagenome predicted proteins. Proteins were predicted from assembled contigs using the Prodigal package.

Supplementary Dataset 3

Compilation of average coverage and protein detections for the different assembled contigs and predicted/annotated proteins by genome bin.

Supplementary Dataset 4

Tab 1 contains the compilation of coverage distribution of identified genes of interest and calculated statistical parameters (mean, standard error, P-value and results of pairwise comparisons). Tab 2 contains the rank distribution of genomes/bins extracted from

Supplementary Dataset 5

Bacterial composition of the metagenome of O. disjuntus. Taxonomy rank is presented at the level of order.

Supplementary Dataset 6

Archaeal composition of the metagenome of O. disjuntus. Taxonomy rank is presented at the level of order.

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Ceja-Navarro, J.A., Karaoz, U., Bill, M. et al. Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle. Nat Microbiol 4, 864–875 (2019). https://doi.org/10.1038/s41564-019-0384-y

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