The microbiome of Folsomia candida: an assessment of bacterial diversity in a Wolbachia-containing animal.
The springtail Folsomia candida is an important model organism for soil ecology, ecotoxicology and ecogenomics. The decomposer activities of soil invertebrates like Folsomia depend on their relationship with microbial communities including gut symbionts. In this paper, we apply high-throughput sequencing to provide a detailed characterization of the bacterial community associated with parthenogenetic F. candida. First, we evaluated a method to suppress the amplification of DNA from the endosymbiont Wolbachia, to prevent it from interfering with the identification of less abundant operational taxonomic units (OTUs). The suppression treatment applied was effective against Wolbachia and did not interfere with the detection of the most abundant OTUs (59 OTUs, contributing over 87% of the reads). However, this method did affect the inferred community composition. Significant differences were subsequently observed in the composition of bacterial communities associated with two different strains of F. candida. A total of 832 OTUs were found, of which 45% were only present in one strain and 17% only in the other. Among the 20 most abundant OTUs, 16 were shared between strains. Denaturing gradient gel electrophoresis and clone libraries, although unable to capture the full diversity of the bacterial community, provided results that supported the NGS data.
Department of Ecological Science, VU University Amsterdam, De Boelelaan 1085-1087, 1081 HV Amsterdam, the Netherlands v.agamennone@vu.nl.
Valeria
V
Agamennone
Department of Ecological Science, VU University Amsterdam, De Boelelaan 1085-1087, 1081 HV Amsterdam, the Netherlands.
Dennis
D
Jakupović
Research Group of Plant and Vegetation Ecology, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium.
James T
JT
Weedon
Department of Ecological Science, VU University Amsterdam, De Boelelaan 1085-1087, 1081 HV Amsterdam, the Netherlands.
Wouter J
WJ
Suring
Department of Ecological Science, VU University Amsterdam, De Boelelaan 1085-1087, 1081 HV Amsterdam, the Netherlands.
Nico M
NM
van Straalen
Department of Ecological Science, VU University Amsterdam, De Boelelaan 1085-1087, 1081 HV Amsterdam, the Netherlands.
Dick
D
Roelofs
Department of Molecular Cell Physiology, VU University Amsterdam, De Boelelaan 1085-1087, 1081 HV Amsterdam, the Netherlands.
Wilfred F M
WF
Röling
D000818:Animals; D001181:Arthropods / Q000382:microbiology* / Q000502:physiology; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D018407:Bacterial Physiological Phenomena; D004269:DNA, Bacterial / Q000235:genetics; D058645:Denaturing Gradient Gel Electrophoresis; D064307:Microbiota; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods; D012987:Soil; D012988:Soil Microbiology; D013559:Symbiosis; D020577:Wolbachia / Q000502:physiology
D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012987:Soil
16S rRNA; Folsomia candida; Illumina sequencing; Wolbachia; bacterial diversity