Molecular analysis of faecal samples from birds to identify potential crop pests and useful biocontrol agents in natural areas

Bull Entomol Res. 2015 Jun;105(3):261-72. doi: 10.1017/S0007485314000935. Epub 2015 Jan 9.


Wild habitats adjoining farmland are potentially valuable sources of natural enemies, but also of pests. Here we tested the utility of birds as 'sampling devices', to identify the diversity of prey available to predators and particularly to screen for pests and natural enemies using natural ecosystems as refugia. Here we used PCR to amplify prey DNA from three sympatric songbirds foraging on small invertebrates in Phragmites reedbed ecosystems, namely the Reed Warbler (Acrocephalus scirpaceus), Sedge Warbler (Acrocephalus schoenobaenus) and Cetti's Warbler (Cettia cetti). A recently described general invertebrate primer pair was used for the first time to analyse diets. Amplicons were cloned and sequenced, then identified by reference to the Barcoding of Life Database and to our own sequences obtained from fresh invertebrates. Forty-five distinct prey DNA sequences were obtained from 11 faecal samples, of which 39 could be identified to species or genus. Targeting three warbler species ensured that species-specific differences in prey choice broadened the range of prey taken. Amongst the prey found in reedbeds were major pests (including the tomato moth Lacanobia oleracea) as well as many potentially valuable natural enemies including aphidophagous hoverflies and braconid wasps. Given the mobility of birds, this approach provides a practical way of sampling a whole habitat at once, providing growers with information on possible invasion by locally resident pests and the colonization potential of natural enemies from local natural habitats.

Keywords: Acrocephalus schoenobaenus; Acrocephalus scirpaceus; Cettia cetti; dietary analysis; reedbed.

MeSH terms

  • Animals
  • Base Sequence
  • Biological Control Agents*
  • Cloning, Molecular
  • DNA / genetics*
  • DNA Barcoding, Taxonomic
  • DNA Primers / genetics
  • Feces / microbiology*
  • Food Chain*
  • Insecta / genetics*
  • Molecular Sequence Data
  • Polymerase Chain Reaction / veterinary
  • Sequence Analysis, DNA / veterinary
  • Songbirds / microbiology*
  • Species Specificity


  • Biological Control Agents
  • DNA Primers
  • DNA