An Insect Herbivore Microbiome with High Plant Biomass-Degrading Capacity

Abstract

Herbivores can gain indirect access to recalcitrant carbon present in plant cell walls through symbiotic associations with lignocellulolytic microbes. A paradigmatic example is the leaf-cutter ant (Tribe: Attini), which uses fresh leaves to cultivate a fungus for food in specialized gardens. Using a combination of sugar composition analyses, metagenomics, and whole-genome sequencing, we reveal that the fungus garden microbiome of leaf-cutter ants is composed of a diverse community of bacteria with high plant biomass-degrading capacity. Comparison of this microbiome's predicted carbohydrate-degrading enzyme profile with other metagenomes shows closest similarity to the bovine rumen, indicating evolutionary convergence of plant biomass degrading potential between two important herbivorous animals. Genomic and physiological characterization of two dominant bacteria in the fungus garden microbiome provides evidence of their capacity to degrade cellulose. Given the recent interest in cellulosic biofuels, understanding how large-scale and rapid plant biomass degradation occurs in a highly evolved insect herbivore is of particular relevance for bioenergy.

Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens

“…The ants presumably gain indirect access to the carbon stored in plant cell walls through the metabolic activities of their fungus gardens, which act as an ancillary digestive system (Pinto-Tomas et al, 2009). Despite being a critical aspect of leaf-cutter ant biology, the process through which fungus gardens degrade plant forage has only recently been intensely investigated (De Fine Licht et al, 2010;Schiott et al, 2010;Suen et al, 2010;Semenova et al, 2011). Originally it was thought that the fungal cultivar primarily degraded cellulose, and that this was the main polymer converted into nutrients for the ants (Martin and Weber, 1969).…”

“…Another study, employing the culture-independent analysis of membrane-lipid markers, has supported the hypothesis that a distinct community of predominantly Gram-negative bacteria resides in fungus gardens , and the presence of symbiotic nitrogen-fixing bacteria in the genera Pantoea and Klebsiella has also been shown (Pinto-Tomas et al, 2009). Together with culture-dependent investigations recovering microbial groups with a broad array of metabolic activities (Bacci et al, 1995;Santos et al, 2004), these experiments have led to the suggestion that fungus gardens represent specialized fungusbacteria consortia selected for by the ants, and that the bacteria have essential roles, including plant biomass degradation, nutrient biosynthesis, and competitive or antibiotic-mediated exclusion of pathogens (Mueller et al, 2005;Haeder et al, 2009;Pinto-Tomas et al, 2009;Suen et al, 2010).…”

“…performed on leaf-cutter ant fungus gardens Suen et al, 2010), but to date only a small quantity of bacterial sequences (B6 Mb) from the fungus gardens of a single ant species have been characterized. Here, by expanding on previous work, we sought to document the non-eukaryotic component of fungus gardens, describe the similarity of communities from different ant species and examine potential microbial activities in situ.…”

An introduction to and a reflection on the “ecogenomics promise”

“…An example is the efficient conversion of cellulose biomass; a key step in the production of second generation biofuels that do not compete with food production. More efficient bioconversion is needed, and metagenomics can help to identify new cellulose processing enzymes or organisms that are able to do this (Brune 2007;Warnecke et al 2007;Ouborg and Kammenga 2008;Suen et al 2010). Leveau (2007) identified several major (overlapping) directions for metagenomics, namely:…”

Contemporary molecular tools in microbial ecology and their application to advancing biotechnology

“…Glycosyl hydrolases Buffalo rumen High-throughput sequencing (Patel, Patel et al 2014) Glycosyl hydrolases Elephant feces High-throughput sequencing (Ilmberger, Gullert et al 2014) Carbohydrate active enzymes Leaf-cutter ant fungus garden High-throughput sequencing (Suen, Scott et al 2010) Glycosyl hydrolases Wallaby High-throughput sequencing, Sanger sequencing (Pope, Denman et al 2010) Antibiotic resistance genes Hen feces High-throughput sequencing (Videnska, Rahman et al 2014) Glycosyl hydrolases Termite hindgut Sanger sequencing, PCR (Warnecke, Luginbuhl et al 2007) …”