Metagenomics: A viable tool for reconstructing herbivore diet

Metagenomics can generate data on the diet of herbivores, without the need for primer selection and PCR enrichment steps as is necessary in metabarcoding. Metagenomic approaches to diet analysis have remained relatively unexplored, requiring validation of bioinformatic steps. Currently, no metagenomic herbivore diet studies have utilized both chloroplast and nuclear markers as reference sequences for plant identification, which would increase the number of reads that could be taxonomically informative. Here, we explore how in silico simulation of metagenomic data sets resembling sequences obtained from faecal samples can be used to validate taxonomic assignment. Using a known list of sequences to create simulated data sets, we derived reliable identification parameters for taxonomic assignments of sequences. We applied these parameters to characterize the diet of western capercaillies (Tetrao urogallus) located in Norway, and compared the results with metabarcoding trnL P6 loop data generated from the same samples. Both methods performed similarly in the number of plant taxa identified (metagenomics 42 taxa, metabarcoding 43 taxa), with no significant difference in species resolution (metagenomics 24%, metabarcoding 23%). We further observed that while metagenomics was strongly affected by the age of faecal samples, with fresh samples outperforming old samples, metabarcoding was not affected by sample age. On the other hand, metagenomics allowed us to simultaneously obtain the mitochondrial genome of the western capercaillies, thereby providing additional ecological information. Our study demonstrates the potential of utilizing metagenomics for diet reconstruction but also highlights key considerations as compared to metabarcoding for future utilization of this technique

The May diet of Capercaillie (Tetrao urogallus) in an extensively logged area of NW Russia

The May crop contents of Capercaillie (Tetrao urogallus) from a highly disturbed (logged) area of NW Russia are documented for the first time. Plants of the tree-shrub layer and bog plants of the field layer together formed the main part of the diets of both cocks (75% of fresh weight) and hens (58%). Fragments of pine (Pinus sylvestris) and bil-berry (Vaccinium myrtillus) were more abundant in crops of cocks, whereas hens con-sumed more young herbaceous shoots and track-side plants. Hens also garnered spruce seeds (Picea spp.) from tracks. Track-side food items formed up to a third of the diet of hens. These included shoots of clover (Trifolium spp.) and especially flower buds of coltsfoot (Tussilago farfara). Complete elimination of some forest tracks, as a manage-ment technique for Capercaillie, could result in a loss of food sources important to hens in most of their Eastern-European range. The closure of tracks from people and vehicles, and their conversion to habitat where spring-blooming plants for hens abundantly grow, seems a more viable conservation option. Even in a highly disturbed area, plants of the na-tive taiga biotopes composed almost all the diet of cocks (ca. 97%). Compared to the cocks, the feeding strategy of hens was more opportunistic; hence, their spring diet may be less vulnerable to logging perturbations