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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

Number of 16S rDNA reads in Log(10) for the 21 bacterial taxa detected in nine plant-specialized biotypes of the pea aphid, Acyrthosiphon pisum.*obligatory symbiont and **facultative symbionts.
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pone.0120664.g001: Number of 16S rDNA reads in Log(10) for the 21 bacterial taxa detected in nine plant-specialized biotypes of the pea aphid, Acyrthosiphon pisum.*obligatory symbiont and **facultative symbionts.

Mentions: Following our selection steps on sequence quality, size and redundancy between PCR replicates, 138,539 sequences were obtained, with a mean of 11,545 reads per sample. Overall, these sequence reads were classified into 21 Operational Taxonomic Units (OTUs). However, only 13 OTUs had a frequency exceeding 0.1% (i.e. approx. 140 reads) among which 3 OTUs represented more than 94% of the sequences. The classification from Greengenes database resulted in 21 unique bacterial genera that belonged to 4 phyla, 6 classes, 8 orders and 14 families (S3 Table). The Proteobacteria represented 51% of these classified bacteria, with the Alphaproteobacteria and the Gammaproteobacteria being the commonest taxa with 25% and 26%, respectively. Among the 138,539 sequences of 400–430 bp, 98% were assigned to bacterial taxa already reported as heritable symbionts of aphids. Spiroplasma was the most represented taxon in number of sequences (48%) followed by Rickettsia (25%) and Buchnera (21%). The frequencies of the other pea aphid symbionts were <2% (Fig 1). We confirmed the presence of Wolbachia, which was recently reported in North American A. pisum by [14], in two pea aphid samples (total frequency of 0.15%). Apart from these symbionts, 454 sequencing detected other bacteria not known to be heritable in arthropods, although most did not exceed 0.1% of sequence reads. Among those with frequencies above 0.1% were Erwinia, Pantoea, Propionibacterium and Ralstonia, each being found in multiple populations and for a total of more than 150 reads each. Erwinia and Pantoea have been described as aphid gut associates [32, 33]. Ralstonia encompass several soil borne plant pathogens that could be ingested or vectorized by aphids. Propionibacterium are usually found in the skin of humans and other animals and their occurrence in our 454 reads may represent contaminants from human handling. Bacterial taxa with read abundance below 0.1% were either plant associates such as Rhizobium and Xanthomonas or environmental/contaminant bacteria.


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)

Number of 16S rDNA reads in Log(10) for the 21 bacterial taxa detected in nine plant-specialized biotypes of the pea aphid, Acyrthosiphon pisum.*obligatory symbiont and **facultative symbionts.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0120664.g001: Number of 16S rDNA reads in Log(10) for the 21 bacterial taxa detected in nine plant-specialized biotypes of the pea aphid, Acyrthosiphon pisum.*obligatory symbiont and **facultative symbionts.
Mentions: Following our selection steps on sequence quality, size and redundancy between PCR replicates, 138,539 sequences were obtained, with a mean of 11,545 reads per sample. Overall, these sequence reads were classified into 21 Operational Taxonomic Units (OTUs). However, only 13 OTUs had a frequency exceeding 0.1% (i.e. approx. 140 reads) among which 3 OTUs represented more than 94% of the sequences. The classification from Greengenes database resulted in 21 unique bacterial genera that belonged to 4 phyla, 6 classes, 8 orders and 14 families (S3 Table). The Proteobacteria represented 51% of these classified bacteria, with the Alphaproteobacteria and the Gammaproteobacteria being the commonest taxa with 25% and 26%, respectively. Among the 138,539 sequences of 400–430 bp, 98% were assigned to bacterial taxa already reported as heritable symbionts of aphids. Spiroplasma was the most represented taxon in number of sequences (48%) followed by Rickettsia (25%) and Buchnera (21%). The frequencies of the other pea aphid symbionts were <2% (Fig 1). We confirmed the presence of Wolbachia, which was recently reported in North American A. pisum by [14], in two pea aphid samples (total frequency of 0.15%). Apart from these symbionts, 454 sequencing detected other bacteria not known to be heritable in arthropods, although most did not exceed 0.1% of sequence reads. Among those with frequencies above 0.1% were Erwinia, Pantoea, Propionibacterium and Ralstonia, each being found in multiple populations and for a total of more than 150 reads each. Erwinia and Pantoea have been described as aphid gut associates [32, 33]. Ralstonia encompass several soil borne plant pathogens that could be ingested or vectorized by aphids. Propionibacterium are usually found in the skin of humans and other animals and their occurrence in our 454 reads may represent contaminants from human handling. Bacterial taxa with read abundance below 0.1% were either plant associates such as Rhizobium and Xanthomonas or environmental/contaminant bacteria.

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