Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics

Autor: Benjamin Linard, David A. Andow, Débora P. Paula, Carmen S. S. Pires, Alfried P. Vogler, Edison R. Sujii
Přispěvatelé: Parque Estaçao Biologica, The Natural History Museum [London] (NHM), University of Minnesota [Twin Cities] (UMN), University of Minnesota System
Rok vydání: 2015
Předmět:
analyte detectability period
MESH: Sequence Analysis
DNA
Mitochondrial DNA
analyte detectability half-life
Molecular Sequence Data
Zoology
Genomics
[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics
Phylogenetics and taxonomy
DNA sequencing
MESH: Predatory Behavior
nuclear genome
MESH: Enterobacteriaceae
Enterobacteriaceae
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Genomics [q-bio.GN]
Botany
MESH: Coleoptera
Genetics
Animals
MESH: Animals
gut content
Ecology
Evolution
Behavior and Systematics
Aphid
MESH: Molecular Sequence Data
biology
mtDNA
Shotgun sequencing
MESH: DNA
food and beverages
DNA
Sequence Analysis
DNA
biochemical phenomena
metabolism
and nutrition
biology.organism_classification
Acyrthosiphon pisum
Coleoptera
Gastrointestinal Tract
aphid
Metagenomics
Aphids
Predatory Behavior
coccinellid
MESH: Gastrointestinal Tract
MESH: Metagenomics
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Buchnera
MESH: Aphids
[SDV.EE.IEO]Life Sciences [q-bio]/Ecology
environment/Symbiosis
Biotechnology
Zdroj: Molecular Ecology Resources
Molecular Ecology Resources, Wiley/Blackwell, 2015, 15 (4), pp.880-892. ⟨10.1111/1755-0998.12364⟩
ISSN: 1755-098X
1755-0998
DOI: 10.1111/1755-0998.12364
Popis: International audience; DNA methods are useful to identify ingested prey items from the gut of predators, but reliable detection is hampered by low amounts of degraded DNA. PCR-based methods can retrieve minute amounts of starting material but suffer from amplification biases and cross-reactions with the predator and related species genomes. Here, we use PCR-free direct shotgun sequencing of total DNA isolated from the gut of the harlequin ladybird Harmonia axyridis at five time points after feeding on a single pea aphid Acyrthosiphon pisum. Sequence reads were matched to three reference databases: Insecta mitogenomes of 587 species, including H. axyridis sequenced here; A. pisum nuclear genome scaffolds; and scaffolds and complete genomes of 13 potential bacterial symbionts. Immediately after feeding , multicopy mtDNA of A. pisum was detected in tens of reads, while hundreds of matches to nuclear scaffolds were detected. Aphid nuclear DNA and mtDNA decayed at similar rates (0.281 and 0.11 h À1 respectively), and the detectability periods were 32.7 and 23.1 h. Metagenomic sequencing also revealed thousands of reads of the obligate Buchnera aphidicola and facultative Regiella insecticola aphid symbionts, which showed exponential decay rates significantly faster than aphid DNA (0.694 and 0.80 h À1 , respectively). However, the facultative aphid symbionts Hamil-tonella defensa, Arsenophonus spp. and Serratia symbiotica showed an unexpected temporary increase in population size by 1–2 orders of magnitude in the predator guts before declining. Metagenomics is a powerful tool that can reveal complex relationships and the dynamics of interactions among predators, prey and their symbionts.
Databáze: OpenAIRE
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