Microbial community structure of leaf-cutter ant fungus gardens and refuse dumps

Abstract

Background: Leaf-cutter ants use fresh plant material to grow a mutualistic fungus that serves as the ants' primary food source. Within fungus gardens, various plant compounds are metabolized and transformed into nutrients suitable for ant consumption. This symbiotic association produces a large amount of refuse consisting primarily of partly degraded plant material. A leaf-cutter ant colony is thus divided into two spatially and chemically distinct environments that together represent a plant biomass degradation gradient. Little is known about the microbial community structure in gardens and dumps or variation between lab and field colonies.

Methodology/principal findings: Using microbial membrane lipid analysis and a variety of community metrics, we assessed and compared the microbiota of fungus gardens and refuse dumps from both laboratory-maintained and field-collected colonies. We found that gardens contained a diverse and consistent community of microbes, dominated by Gram-negative bacteria, particularly gamma-Proteobacteria and Bacteroidetes. These findings were consistent across lab and field gardens, as well as host ant taxa. In contrast, dumps were enriched for Gram-positive and anaerobic bacteria. Broad-scale clustering analyses revealed that community relatedness between samples reflected system component (gardens/dumps) rather than colony source (lab/field). At finer scales samples clustered according to colony source.

Conclusions/significance: Here we report the first comparative analysis of the microbiota from leaf-cutter ant colonies. Our work reveals the presence of two distinct communities: one in the fungus garden and the other in the refuse dump. Though we find some effect of colony source on community structure, our data indicate the presence of consistently associated microbes within gardens and dumps. Substrate composition and system component appear to be the most important factor in structuring the microbial communities. These results thus suggest that resident communities are shaped by the plant degradation gradient created by ant behavior, specifically their fungiculture and waste management.

Figure 1. Representation of the leaf-cutter ant system.

(A) Fresh plant material is harvested by foraging workers and brought back to the nest. (B) Plant material is processed and incorporated into the top of the garden, where it serves as the primary growth substrate for the mutualistic fungus. Substrate processing occurs over the course of several weeks and enzymatic analyses suggest that the fungus garden contains a decompositional gradient where more easily utilized material is extracted at the top of the garden and more recalcitrant material remains and appears to be partailly degraded at the garden bottom , . (C) Older substrate and spent fungal material are removed from the bottom of the garden and transported to a refuse dump. Older workers manipulate material on the refuse dump presuambly to facilitate dgradation of the material . (D) Typical lab colony set-up showing the relative orientation of the fungus garden and refuse dump. Gardens and dumps are housed in individual chambers within a larger box.

Figure 2. Rarefaction and lipid accumulation curves.

Observed and estimated lipid richness of Lab colonies (gardens vs. dumps) and Field colonies (gardens vs. dumps).

Figure 3. Contribution of major lipid classes to community structure.

Chart showing the relative contribution of chemically-related lipid classes to lipid profile of gardens (G) and dumps (D) from lab and field colonies. In addition to ‘Unclassified’ lipids (U), gardens predominately contain saturated (SFA), monounsaturated (MUFA), and hydroxyl (HFA) fatty acids. Dumps also contain these lipid classes but are enriched for cyclic (CyFA), branched (BrFA), methylated (MeFA) and polyunsaturated (PUFA) fatty acids. These data suggest a broad-scale shift in community structure from fungus gardens to refuse dumps as well as community similarity between respective components of lab and field colonies.

Figure 4. Principal Component Analysis (PCA) of lipid markers recovered from the four sample types.

PCA were used to access differences among the four major comparisons explored in this study. Only the first two principal components are shown in all cases (PC1 and PC2). (A) Field gardens and field dumps clustered along PC1 however there was considerable variation among dump samples along both principal components. (B) From lab samples, clustering along PC1 was related to microhabitat type (garden or dump) and clustering along PC2 was related to year of sampling (2006 or 2008). Solid line indicates dump samples and dashed line indicates garden samples. (C) PCA of garden samples showed that variation along PC1 was related to sample source (lab or field). (D) PCA of dumps showed a similar pattern in that separation along PC1 was related to sample source. Lab dumps formed a tight cluster likely due in part to the large variation among field samples. Abbreviations: LG-06, 2006 lab garden; LG-08, 2008 lab gardens; FG, field garden; LD-06, 2006 lab dumps; LD-08, 2008 lab dumps; FD, field dumps.

Figure 5. Heat map and dendrograms of lipid distribution.

A heat map of samples by lipids. The heat map is arranged according to sample and lipid clustering analysis and mol% values were arcsine-transformed. The dendrogram for the samples (vertical) was calculated using the total number of lipid biomarkers present in each sample. For simplicity, only named lipids were used for the lipid dendrogram (horizontal) and thus for the heat map. Green lines in the vertical dendrogram indicate samples from Atta colonies and red lines indicate samples from Acromyrmex colonies. Sample codes are as follows: lab (L), field (F), garden (G), and dump (D). Numbers indicate colony identification and the extensions (-06) and (-08) indicate year of sampling. Clustering analysis of samples shows two distinct groups. Group SI contains only garden samples and group SII contains only dump samples. Within each group, samples generally cluster according to source (lab or field), however two dump samples from lab colonies cluster with the field dumps (LD3-06 and LD7-06 in bold). Overall, field dumps exhibit the highest taxon diversity across lipid groups LI and LII. Generally, garden communities are well represented by group LII taxa and dumps, especially from lab colonies, are dominated by group LI taxa. Group LI contains primarily branched (iso and antiso) lipids, indicative of Gram-positive bacteria . Group LII is high in hydroxyl lipids and monounsaturated fatty acids, which indicate Gram-negative bacteria . Garden samples, in particular, are enriched with these lipid markers.