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Analysis of Extensive [FeFe] Hydrogenase Gene Diversity Within the Gut Microbiota of Insects Representing Five Families of Dictyoptera

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Abstract

We have designed and utilized degenerate primers in the phylogenetic analysis of [FeFe] hydrogenase gene diversity in the gut ecosystems of roaches and lower termites. H2 is an important free intermediate in the breakdown of wood by termite gut microbial communities, reaching concentrations in some species exceeding those measured for any other biological system. The primers designed target with specificity the largest group of enzymatic H domain proteins previously identified in a termite gut metagenome. “Family 3” hydrogenase sequences were amplified from the guts of lower termites, Incisitermes minor, Zootermopsis nevadensis, and Reticulitermes hesperus, and two roaches, Cryptocercus punctulatus and Periplaneta americana. Subsequent analyses revealed that all termite and Cryptocercus sequences were phylogenetically distinct from non-termite-associated hydrogenases available from public databases. The abundance of unique sequence operational taxonomic units (as many as 21 from each species) underscores the previously demonstrated physiological importance of H2 to the gut ecosystems of these wood-feeding insects. The diversity of sequences observed might be reflective of multiple niches that the enzymes have been evolved to accommodate. Sequences cloned from Cryptocercus and the lower termite samples, all of which are wood feeding insects, clustered closely with one another in phylogenetic analyses to the exclusion of alleles from P. americana, an omnivorous cockroach, also cloned during this study. We present primers targeting a family of termite gut [FeFe] hydrogenases and provide results that are consistent with a pivotal role for hydrogen in the termite gut ecosystem and point toward unique evolutionary adaptations to the gut ecosystem.

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Acknowledgments

This research was supported by grants from the NSF (MCB-0523267) and the DOE (DE-FG02-07ER64484) and by an NSF Graduate Student Research Fellowship (to NRB). We would like to thank our laboratory colleagues and several anonymous reviewers for their insightful comments during the preparation of this manuscript.

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  1. Biochemistry and Molecular Biophysics, California Institute of Technology, M/C 138-78, Pasadena, CA, 91125, USA

    Nicholas R. Ballor & Jared R. Leadbetter

  2. Ronald and Maxine Linde Center for Global Environmental Science, California Institute of Technology, M/C 138-78, Pasadena, CA, 91125, USA

    Jared R. Leadbetter

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Correspondence to Jared R. Leadbetter.

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Figure S1

Maximum likelihood tree of all cloned family 3 [FeFe] hydrogenase sequences. The tree was calculated using a maximum likelihood (Phylip ProML) method with 173 unambiguously aligned amino acid positions. Open circles designate groupings also supported by either parsimony (Phylip PROTPARS, 1,000 bootstraps) or distance matrix (Fitch) methods. Closed circles designate groupings supported by all three methods. Hydrogenase sequences taken from T. primitia ZAS-2 and T. primitia ZAS-9 are labeled as ZAS-2 (HndA1) and ZAS-9 (HndA), respectively. The sequence labeled as Metagenome corresponds to the sequence with the gene identifier 2004084376 taken from a termite hindgut metagenome sequence [33]. Outgroup sequences are listed in the “Methods” section of the main text. (JPEG 608 kb)

High resolution image (EPS 351 kb)

Figure S2

Phylogram of family 3 [FeFe] hydrogenases cloned from the guts of an adult and nymph C. punctulatus samples. The tree was calculated using a maximum likelihood (Phylip ProML) method with 173 unambiguously aligned amino acid positions. Open circles designate groupings also supported by either parsimony (Phylip PROTPARS, 1,000 bootstraps) or distance matrix (Fitch) methods. Closed circles designate groupings supported by all three methods. All sequences cloned from P. americana are highlighted by a gray box. Outgroup sequences are listed in the “Methods” section of the main text. (JPEG 264 kb)

High resolution image (EPS 325 kb)

Table S1

OTUs calculated using the furthest-neighbor method in DOTUR (Schloss & Handelsman, 2005) with a 97% amino-acid similarity cut-off. Number of cloned sequences grouped within each OTU. Percent of cloned sequences represented by each OTU within a gut sample. §Sequences that could not be classified as belonging to any of the sequence families defined by Warnecke et al. [33]. Sequence classified as belonging to the Family 7 hydrogenase sequence family defined by Warnecke et al. [33]. (PDF 459 kb)

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Ballor, N.R., Leadbetter, J.R. Analysis of Extensive [FeFe] Hydrogenase Gene Diversity Within the Gut Microbiota of Insects Representing Five Families of Dictyoptera. Microb Ecol 63, 586–595 (2012). https://doi.org/10.1007/s00248-011-9941-5

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