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Bacterial communities associated with host-adapted populations of pea aphids revealed by deep sequencing of 16S ribosomal DNA.

Gauthier JP, Outreman Y, Mieuzet L, Simon JC - PLoS ONE (2015)

Bottom Line: Associations between microbes and animals are ubiquitous and hosts may benefit from harbouring microbial communities through improved resource exploitation or resistance to environmental stress.The presence of Wolbachia was confirmed in A. pisum while Erwinia and Pantoea, two gut associates, were detected in multiple samples.Bacterial communities differed more between than within biotypes but this difference did not correlate with the genetic divergence between biotypes.

View Article: PubMed Central - PubMed

Affiliation: INRA, UMR 1349 IGEPP "Institut de Génétique, Environnement et Protection des Plantes", 35653, Le Rheu, France.

ABSTRACT
Associations between microbes and animals are ubiquitous and hosts may benefit from harbouring microbial communities through improved resource exploitation or resistance to environmental stress. The pea aphid, Acyrthosiphon pisum, is the host of heritable bacterial symbionts, including the obligate endosymbiont Buchnera aphidicola and several facultative symbionts. While obligate symbionts supply aphids with key nutrients, facultative symbionts influence their hosts in many ways such as protection against natural enemies, heat tolerance, color change and reproduction alteration. The pea aphid also encompasses multiple plant-specialized biotypes, each adapted to one or a few legume species. Facultative symbiont communities differ strongly between biotypes, although bacterial involvement in plant specialization is uncertain. Here, we analyse the diversity of bacterial communities associated with nine biotypes of the pea aphid complex using amplicon pyrosequencing of 16S rRNA genes. Combined clustering and phylogenetic analyses of 16S sequences allowed identifying 21 bacterial OTUs (Operational Taxonomic Unit). More than 98% of the sequencing reads were assigned to known pea aphid symbionts. The presence of Wolbachia was confirmed in A. pisum while Erwinia and Pantoea, two gut associates, were detected in multiple samples. The diversity of bacterial communities harboured by pea aphid biotypes was very low, ranging from 3 to 11 OTUs across samples. Bacterial communities differed more between than within biotypes but this difference did not correlate with the genetic divergence between biotypes. Altogether, these results confirm that the aphid microbiota is dominated by a few heritable symbionts and that plant specialization is an important structuring factor of bacterial communities associated with the pea aphid complex. However, since we examined the microbiota of aphid samples kept a few generations in controlled conditions, it may be that bacterial diversity was underestimated due to the possible loss of environmental or transient taxa.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic analysis of 16S rDNA based on a Neighbor-Joining tree relating bacterial sequences from references selected in GenBank (REF) and from 454 amplicon sequencing of populations and biotypes of the pea aphid complex.Accession numbers of representative sequences of each OTU found in the different samples (74 sequences in total) are given in Supporting Information (S3 Table).
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pone.0120664.g002: Phylogenetic analysis of 16S rDNA based on a Neighbor-Joining tree relating bacterial sequences from references selected in GenBank (REF) and from 454 amplicon sequencing of populations and biotypes of the pea aphid complex.Accession numbers of representative sequences of each OTU found in the different samples (74 sequences in total) are given in Supporting Information (S3 Table).

Mentions: Taxonomic assignment based on the Greengenes database was very well supported by the Neighbor-Joining tree of 16S rDNA sequences from our 454 dataset and from references selected in GenBank (Fig 2). OTUs assigned to reported aphid symbionts clustered with the reference sequence from a pea aphid host. None of our 454 sequences grouped with the PAXS reference, probably because this recently described pea aphid symbiont was not detected due to poor sequence identity with our universal primers (sequence homology with PAXS was 100% for the reverse primer but only 60% for the forward primer). Erwinia and Pantoea appear as two distinct clades on the phylogenetic tree. Globally, there was a significant range of 16S rDNA variation within bacterial taxa, which could be due to either sequence errors in both 454 and Genbank sequences or variation between strains of bacterial taxa from different populations or biotypes of A. pisum.


Bacterial communities associated with host-adapted populations of pea aphids revealed by deep sequencing of 16S ribosomal DNA.

Gauthier JP, Outreman Y, Mieuzet L, Simon JC - PLoS ONE (2015)

Phylogenetic analysis of 16S rDNA based on a Neighbor-Joining tree relating bacterial sequences from references selected in GenBank (REF) and from 454 amplicon sequencing of populations and biotypes of the pea aphid complex.Accession numbers of representative sequences of each OTU found in the different samples (74 sequences in total) are given in Supporting Information (S3 Table).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4373712&req=5

pone.0120664.g002: Phylogenetic analysis of 16S rDNA based on a Neighbor-Joining tree relating bacterial sequences from references selected in GenBank (REF) and from 454 amplicon sequencing of populations and biotypes of the pea aphid complex.Accession numbers of representative sequences of each OTU found in the different samples (74 sequences in total) are given in Supporting Information (S3 Table).
Mentions: Taxonomic assignment based on the Greengenes database was very well supported by the Neighbor-Joining tree of 16S rDNA sequences from our 454 dataset and from references selected in GenBank (Fig 2). OTUs assigned to reported aphid symbionts clustered with the reference sequence from a pea aphid host. None of our 454 sequences grouped with the PAXS reference, probably because this recently described pea aphid symbiont was not detected due to poor sequence identity with our universal primers (sequence homology with PAXS was 100% for the reverse primer but only 60% for the forward primer). Erwinia and Pantoea appear as two distinct clades on the phylogenetic tree. Globally, there was a significant range of 16S rDNA variation within bacterial taxa, which could be due to either sequence errors in both 454 and Genbank sequences or variation between strains of bacterial taxa from different populations or biotypes of A. pisum.

Bottom Line: Associations between microbes and animals are ubiquitous and hosts may benefit from harbouring microbial communities through improved resource exploitation or resistance to environmental stress.The presence of Wolbachia was confirmed in A. pisum while Erwinia and Pantoea, two gut associates, were detected in multiple samples.Bacterial communities differed more between than within biotypes but this difference did not correlate with the genetic divergence between biotypes.

View Article: PubMed Central - PubMed

Affiliation: INRA, UMR 1349 IGEPP "Institut de Génétique, Environnement et Protection des Plantes", 35653, Le Rheu, France.

ABSTRACT
Associations between microbes and animals are ubiquitous and hosts may benefit from harbouring microbial communities through improved resource exploitation or resistance to environmental stress. The pea aphid, Acyrthosiphon pisum, is the host of heritable bacterial symbionts, including the obligate endosymbiont Buchnera aphidicola and several facultative symbionts. While obligate symbionts supply aphids with key nutrients, facultative symbionts influence their hosts in many ways such as protection against natural enemies, heat tolerance, color change and reproduction alteration. The pea aphid also encompasses multiple plant-specialized biotypes, each adapted to one or a few legume species. Facultative symbiont communities differ strongly between biotypes, although bacterial involvement in plant specialization is uncertain. Here, we analyse the diversity of bacterial communities associated with nine biotypes of the pea aphid complex using amplicon pyrosequencing of 16S rRNA genes. Combined clustering and phylogenetic analyses of 16S sequences allowed identifying 21 bacterial OTUs (Operational Taxonomic Unit). More than 98% of the sequencing reads were assigned to known pea aphid symbionts. The presence of Wolbachia was confirmed in A. pisum while Erwinia and Pantoea, two gut associates, were detected in multiple samples. The diversity of bacterial communities harboured by pea aphid biotypes was very low, ranging from 3 to 11 OTUs across samples. Bacterial communities differed more between than within biotypes but this difference did not correlate with the genetic divergence between biotypes. Altogether, these results confirm that the aphid microbiota is dominated by a few heritable symbionts and that plant specialization is an important structuring factor of bacterial communities associated with the pea aphid complex. However, since we examined the microbiota of aphid samples kept a few generations in controlled conditions, it may be that bacterial diversity was underestimated due to the possible loss of environmental or transient taxa.

No MeSH data available.


Related in: MedlinePlus