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.
This is a preview of subscription content
Subscribe to Nature+
Get immediate online access to the entire Nature family of 50+ journals
Subscribe to Journal
Get full journal access for 1 year
only $9.92 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Get time limited or full article access on ReadCube.
All prices are NET prices.
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/.
Shapira, M. Gut microbiotas and host evolution: scaling up symbiosis. Trends Ecol. Evol. 31, 539–549 (2016).
Beran, F. & Gershenzon, J. Microbes matter: herbivore gut endosymbionts play a role in breakdown of host plant toxins. Environ. Microbiol. 18, 1306–1307 (2016).
Ceja-Navarro, J. A. et al. Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee.Nat. Commun. 6, 7618 (2015).
Warnecke, F. et al. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450, 560–565 (2007).
Schmitt-Wagner, D. & Brune, A. Hydrogen profiles and localization of methanogenic activities in the highly compartmentalized hindgut of soil-feeding higher termites (Cubitermes spp.). Appl. Environ. Microbiol. 65, 4490–4496 (1999).
Lemke, T., van Alen, T., Hackstein, J. H. P. & Brune, A. Cross-epithelial hydrogen transfer from the midgut compartment drives methanogenesis in the hindgut of cockroaches. Appl. Environ. Microbiol. 67, 4657–4661 (2001).
Pester, M. & Brune, A. Hydrogen is the central free intermediate during lignocellulose degradation by termite gut symbionts. ISME J. 1, 551–565 (2007).
Kohler, T., Dietrich, C., Scheffrahn, R. H. & Brune, A. High-resolution analysis of gut environment and bacterial microbiota reveals functional compartmentation of the gut in wood-feeding higher termites (Nasutitermes spp.). Appl. Environ. Microbiol. 78, 4691–4701 (2012).
Dietrich, C., Kohler, T. & Brune, A. The cockroach origin of the termite gut microbiota: patterns in bacterial community structure reflect major evolutionary events. Appl. Environ. Microbiol. 80, 2261–2269 (2014).
Ceja-Navarro, J. A. et al. Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut of Odontotaenius disjunctus. ISME J. 8, 6–18 (2014).
Schuster, J. C. & Schuster, L. B. Social behavior in passalid beetles (Coleoptera: Passalidae): cooperative brood care. Florida Entomol. 68, 266–272 (1985).
Wicknick, J. A. & Miskelly, S. A. Behavioral interactions between non-cohabiting bess beetles, Odontotaenius disjunctus (Illiger) (Coleoptera: Passalidae). Coleopt. Bull. 63, 108–116 (2009).
Schuster, J. C. & Schuster, L. B. in The Evolution of Social Behavior in Insects and Arachnids (eds by Choe, J. C. & Crespi, B. J.) 260–269 (Cambridge Univ. Press, 1997).
Lindblad, I. Wood-inhabiting fungi on fallen logs of Norway spruce: relations to forest management and substrate quality. Nord. J. Bot. 18, 243–255 (1998).
Nardi, J. B. et al. Communities of microbes that inhabit the changing hindgut landscape of a subsocial beetle. Arthropod Struct. Dev. 35, 57–68 (2006).
Castillo, M. L. & Reyes-Castillo, P. in Tropical Biology and Conservation Management. Encyclopedia of Life Support Systems Vol. VII (eds Del Claro, K., Oliveira, P. S. & Rico-Gray, V.) 112–133 (2009).
Ulyshen, M. D. Wood decomposition as influenced by invertebrates.Biol. Rev. Camb. Phil. Soc. 91, 70–85 (2014).
Pearse, A. S., Patterson, M. T., Rankin, J. S. & Wharton, G. W. The ecology of Passalus cornutus Fabricius, a beetle which lives in rotting logs. Ecol. Monogr. 6, 455–490 (1936).
Urbina, H. & Blackwell, M. Multilocus phylogenetic study of the Scheffersomyces yeast clade and characterization of the N-terminal region of xylose reductase gene. PLoS ONE. 7, e39128 (2012).
Lichtwardt, R. W., White, M. M., Cafaro, M. J. & Misra, J. K. Fungi associated with passalid beetles and their mites. Mycologia 91, 694–702 (1999).
Suh, S. O., Marshall, C. J., McHugh, J. V. & Blackwell, M. Wood ingestion by passalid beetles in the presence of xylose-fermenting gut yeasts. Mol. Ecol. 12, 3137–3145 (2003).
Zhang, N., Suh, S.-O. & Blackwell, M. Microorganisms in the gut of beetles: evidence from molecular cloning. J. Invertebr. Pathol. 84, 226–233 (2003).
Nguyen, N. H., Suh, S.-O., Marshall, C. J. & Blackwell, M. Morphological and ecological similarities: wood-boring beetles associated with novel xylose-fermenting yeasts, Spathaspora passalidarum gen. sp. nov. and Candida jeffriesii sp. nov. Mycol. Res. 110, 1232–1241 (2006).
Urbina, H., Schuster, J. & Blackwell, M. The gut of Guatemalan passalid beetles: a habitat colonized by cellobiose- and xylose-fermenting yeasts. Fungal Ecol. 6, 339–355 (2013).
Geib, S. M. et al. Lignin degradation in wood-feeding insects. Proc. Natl Acad. Sci. USA 105, 12932–12937 (2008).
De Gonzalo, G., Colpa, D. I., Habib, M. H. M. & Fraaije, M. W. Bacterial enzymes involved in lignin degradation. J. Biotechnol. 236, 110–119 (2016).
Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P. M. & Henrissat, B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42, D490–D495 (2014).
Sabbadin, F. et al. An ancient family of lytic polysaccharide monooxygenases with roles in arthropod development and biomass digestion. Nat. Commun. 9, 756 (2018).
Cord-Ruwisch, R., Seitz, H.-J. & Conrad, R. The capacity of hydrogenotrophic anaerobic bacteria to compete for traces of hydrogen depends on the redox potential of the terminal electron acceptor. Arch. Microbiol. 149, 350–357 (1988).
Hoehler, T. M., Alperin, M. J., Albert, D. B. & Martens, C. S. Thermodynamic control on hydrogen concentrations in anoxic sediments. Geochim. Cosmochim. Acta 62, 1745–1756 (1998).
Douglas, A. E. Multiorganismal insects: diversity and function of resident microorganisms. Annu. Rev. Entomol. 60, 17–34 (2014).
Tarmadi, D. et al. The effects of various lignocelluloses and lignins on physiological responses of a lower termite, Coptotermes formosanus. J. Wood Sci. 63, 464–472 (2017).
Zhou, J. et al. Diversity, roles, and biotechnological applications of symbiotic microorganisms in the gut of termite. Curr. Microbiol. https://doi.org/10.1007/s00284-018-1502-4 (2018).
Brune, A. Symbiotic digestion of lignocellulose in termite guts. Nat. Rev. Microbiol. 12, 168–180 (2014).
Shabat, S. K. et al. Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants. ISME J. 10, 2958–2972 (2016).
Scully, E. D., Hoover, K., Carlson, J. E., Tien, M. & Geib, S. M. Midgut transcriptome profiling of Anoplophora glabripennis, a lignocellulose degrading cerambycid beetle. BMC Genomics 14, 850 (2013).
Abdul Rahman, N. et al. A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes. Microbiome 3, 5 (2015).
Zhou, M. et al. Assessment of microbiome changes after rumen transfaunation: implications on improving feed efficiency in beef cattle. Microbiome 6, 62 (2018).
Westneat, M. W. et al. Tracheal respiration in insects visualized with synchrotron X-ray imaging. Science 299, 558–560 (2003).
Jackson, H. B., Baum, K. A., Robert, T. & Cronin, J. T. Habitat-specific movement and edge-mediated behavior of the saproxylic insect Odontotaenius disjunctus (Coleoptera: Passalidae). Environ. Entomol. 38, 1411–1422 (2009).
King, A. & Fashing, N. Infanticidal behavior in the subsocial beetle Odontotaenius disjunctus (Illiger) (Coleoptera: Passalidae). J. Insect Behav. 20, 527–536 (2007).
Krause, J. B. & Ryan, M. T. The stages of development in the embryology of the horned passalus beetle, Popilius disjunctus Illiger. Ann. Entomol. Soc. Am. 46, 1–20 (1953).
R Core Development Team R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2013).
Bligh, E. G. & Dyer, W. J. A rapid method of total lipid extraction and purification. Can. J. Biochem. Physiol. 37, 911–917 (1959).
Boisvert, S., Raymond, F., Godzaridis, É., Laviolette, F. & Corbeil, J. Ray Meta: scalable de novo metagenome assembly and profiling. Genome. Biol. 13, R122 (2012).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).
Eddy, S. R. A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput. Biol. 4, e1000069 (2008).
Kelly, R. T. et al. Chemically etched open tubular and monolithic emitters for nanoelectrospray ionization mass spectrometry. Anal. Chem. 78, 7796–7801 (2006).
Maiolica, A., Borsotti, D. & Rappsilber, J. Self-made frits for nanoscale columns in proteomics. Proteomics 5, 3847–3850 (2005).
Kim, Y.-M. et al. Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms.Front. Microbiol. 6, 209 (2015).
Hiller, K. et al. Metabolitedetector: comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis. Anal. Chem. 81, 3429–3439 (2009).
Alneberg, J. et al. Binning metagenomic contigs by coverage and composition. Nat. Methods 11, 1144–1146 (2014).
Darling, A. E. et al. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ. 2, e243 (2014).
Kerepesi, C., Bánky, D. & Grolmusz, V. AmphoraNet: the webserver implementation of the AMPHORA2 metagenomic workflow suite. Gene 533, 538–540 (2014).
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.
The authors declare no competing interests.
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Figures 1–5, Supplementary Tables 1–3 and legends for Supplementary Datasets.
Fasta file containing all metagenome-assembled contigs.
Fasta file containing all the metagenome predicted proteins. Proteins were predicted from assembled contigs using the Prodigal package.
Compilation of average coverage and protein detections for the different assembled contigs and predicted/annotated proteins by genome bin.
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
Bacterial composition of the metagenome of O. disjuntus. Taxonomy rank is presented at the level of order.
Archaeal composition of the metagenome of O. disjuntus. Taxonomy rank is presented at the level of order.
About this article
Cite this article
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
Structural basis of lignocellulose deconstruction by the wood-feeding anobiid beetle Nicobium hirtum
Journal of Wood Science (2022)
Spectroscopic analysis reveals that soil phosphorus availability and plant allocation strategies impact feedstock quality of nutrient-limited switchgrass
Communications Biology (2022)
Intestinal microbiota and functional characteristics of black soldier fly larvae (Hermetia illucens)
Annals of Microbiology (2021)
A novel d-xylose isomerase from the gut of the wood feeding beetle Odontotaenius disjunctus efficiently expressed in Saccharomyces cerevisiae
Scientific Reports (2021)
Description of Vagococcus coleopterorum sp. nov., isolated from the intestine of the diving beetle, Cybister lewisianus, and Vagococcus hydrophili sp. nov., isolated from the intestine of the dark diving beetle, Hydrophilus acuminatus, and emended description of the genus Vagococcus
Journal of Microbiology (2021)