Kautz S, Rubin BER, Russell JA, Moreaua CS.. Surveying the microbiome of ants: Comparing 454 pyrosequencing with traditional methods to uncover bacterial diversity. Appl Environ Microbiol 79: 525-534

Field Museum of Natural History, Department of Zoology, 1400 S. Lake Shore Dr., Chicago, IL 60605, USA.
Applied and Environmental Microbiology (Impact Factor: 3.67). 11/2012; 79(2). DOI: 10.1128/AEM.03107-12
Source: PubMed

ABSTRACT

We are only beginning to understand the depth and breadth of microbial associations across the eukaryotic tree of life. Reliably
assessing bacterial diversity is a key challenge, and next-generation sequencing approaches are facilitating this endeavor.
In this study, we used 16S rRNA amplicon pyrosequencing to survey microbial diversity in ants. We compared 454 libraries with
Sanger-sequenced clone libraries as well as cultivation of live bacteria. Pyrosequencing yielded 95,656 bacterial 16S rRNA
reads from 19 samples derived from four colonies of one ant species. The most dominant bacterial orders in the microbiome
of the turtle ant Cephalotes varians were Rhizobiales, Burkholderiales, Opitutales, Xanthomonadales, and Campylobacterales, as revealed through both 454 sequencing and cloning. Even after stringent quality filtering, pyrosequencing recovered 445
microbe operational taxonomic units (OTUs) not detected with traditional techniques. In comparing bacterial communities associated
with specific tissues, we found that gut tissues had significantly higher diversity than nongut tissues, and many of the OTUs
identified from these groups clustered within ant-specific lineages, indicating a deep coevolutionary history of Cephalotes ants and their associated microbes. These lineages likely function as nutritional symbionts. One of four ant colonies investigated
was infected with a Spiroplasma sp. (order Entomoplasmatales), a potential ant pathogen. Our work shows that the microbiome associated with Cephalotes varians is dominated by a few dozen bacterial lineages and that 454 sequencing is a cost-efficient tool to screen ant symbiont diversity.

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    • "The emergence of ecologically dominant canopy ants has been facilitated by mutualisms with gut microbes that enable colonies to persist on a low-N diet (Eilmus & Heil, 2009;Russell et al., 2009;Anderson et al., 2012). Paraponera clavata colonies are highly variable in the amount of prey found in their diet (Tillberg & Breed, 2004), probably more so than other canopy-foraging ants (Blüthgen et al., 2003), and do not appear to have a consistent gut microbiome as other canopy specialists (Kautz et al., 2013). Nonetheless, a symbiotic Rhizobiales bacterium, which is likely to pay a role in N recycling, is positively associated with a carbohydrate-biased diet of P. clavata, and increases in prevalence along with the experimental addition of sugar water to the diet of the ants (Larson et al., 2014). "
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    ABSTRACT: 1.Canopy-foragingantshavecarbohydrate-richdietsandthestoichiometric excess of carbon may result in energetic allocation decisions that facilitate ecological dominance. 2. If dietary carbohydrates facilitate ecological dominance in canopy ants, then the mechanism for this relationship is unknown. 3. Four hypotheses were posit that may explain how a carbohydrate-rich diet might facilitate ecological dominance in canopy ants: Aggressive Defense, Metabolic Fuel, Foraging Success, and Prey Acquisition. 4. To assess these hypotheses, experiments were conducted on the canopy-foraging bullet ant, Paraponera clavata (Fabricius), an omnivorous species that demonstrates high variability in the relative contribution of carbohydrates to the diets of colonies. 5. No support was found for the Aggressive Defense, Metabolic Fuel and Prey Acquisition hypotheses. 6. The Foraging Success hypothesis was supported, as the proportion of nectar in the diet predicted the overall foraging success. 7. It was argued that there is no explicit advantage in the exploitation of nectar over other food resources, other than the fact that it is the most accessible food resource in the rainforest canopy. Keywords. Aggression,competition,density,foraging,nectar,omnivory,Paraponera, predation, tempo.
    Full-text · Article · Jan 2016 · Ecological Entomology
    • "Nowadays, next generation sequencing (NGS) offers the opportunity to determine the compositions of bacterial communities in great detail. This has proven to be an effective tool to identify some rare groups that were not easily detected with older methods (Kautz et al. 2013). "
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    ABSTRACT: The springtail Folsomia candida is an important model organism for soil ecology, ecotoxicology and ecogenomics. The decomposer activities of soil invertebrates like Folsomia depend on their relationship with microbial communities including gut symbionts. In this paper, we apply high-throughput sequencing to provide a detailed characterization of the bacterial community associated with parthenogenetic F. candida. First, we evaluated a method to suppress the amplification of DNA from the endosymbiont Wolbachia, to prevent it from interfering with the identification of less abundant Operational Taxonomic Units (OTUs). The suppression treatment applied was effective against Wolbachia and did not interfere with the detection of the most abundant OTUs (59 OTUs, contributing over 87% of the reads). However, this method did affect the inferred community composition. Significant differences were subsequently observed in the composition of bacterial communities associated with two different strains of F. candida. A total of 832 OTUs were found, of which 45% were only present in one strain and 17% only in the other. Among the 20 most abundant OTUs 16 were shared between strains. Denaturing Gradient Gel Electrophoresis (DGGE) and clone libraries, although unable to capture the full diversity of the bacterial community, provided results that supported the NGS data.
    No preview · Article · Oct 2015 · FEMS Microbiology Ecology
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    • "This is the first genus-wide survey with broad phylogenetic sampling for Cephalotes and is consistent with previous results from small numbers of species (C. atratus, C. rohweri and C. varians; see Russell et al. 2009; Anderson et al. 2012; Kautz et al. 2013). These communities appear to be relatively simple, averaging just 20 unique 97% OTUs per 1000 sequences (Fig. S2, Table S3, Supporting information). "

    Full-text · Dataset · Jul 2015
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