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Plant-bacteria association and symbiosis: are there common genomic traits in alphaproteobacteria?

Pini F, Galardini M, Bazzicalupo M, Mengoni A - Genes (Basel) (2011)

Bottom Line: To shed some light on possible common genetic features in such a heterogeneous set of plant associations, the genomes of 92 Alphaproteobacteria strains were analyzed with a fuzzy orthologs-species detection approach.Two of these orthologous groups were also detected in fully sequenced plant-associated Betaproteobacteria and Gammaproteobacteria.Overall these results lead us to hypothesize that plant-bacteria associations, though quite variable, are partially supported by a conserved set of unsuspected gene functions.

View Article: PubMed Central - PubMed

Affiliation: Department of Evolutionary Biology, University of Florence, via Romana 17, 50125 Firenze, Italy. francesco.pini@unifi.it.

ABSTRACT
Alphaproteobacteria show a great versatility in adapting to a broad range of environments and lifestyles, with the association between bacteria and plants as one of the most intriguing, spanning from relatively unspecific nonsymbiotic association (as rhizospheric or endophytic strains) to the highly species-specific interaction of rhizobia. To shed some light on possible common genetic features in such a heterogeneous set of plant associations, the genomes of 92 Alphaproteobacteria strains were analyzed with a fuzzy orthologs-species detection approach. This showed that the different habitats and lifestyles of plant-associated bacteria (soil, plant colonizers, symbiont) are partially reflected by the trend to have larger genomes with respect to nonplant-associated species. A relatively large set of genes specific to symbiotic bacteria (73 orthologous groups) was found, with a remarkable presence of regulators, sugar transporters, metabolic enzymes, nodulation genes and several genes with unknown function that could be good candidates for further characterization. Interestingly, 15 orthologous groupspresent in all plant-associated bacteria (symbiotic and nonsymbiotic), but absent in nonplant-associated bacteria, were also found, whose functions were mainly related to regulation of gene expression and electron transport. Two of these orthologous groups were also detected in fully sequenced plant-associated Betaproteobacteria and Gammaproteobacteria. Overall these results lead us to hypothesize that plant-bacteria associations, though quite variable, are partially supported by a conserved set of unsuspected gene functions.

No MeSH data available.


Phylogenetic tree based on 16S rRNA gene sequence for the 92 selected organisms. Names in green and cyan indicate plant-associated species (green, symbionts; cyan, nonsymbionts). The dimension of the circles is proportional to the genome size, while the color of the circles indicates the GC content.
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f1-genes-02-01017: Phylogenetic tree based on 16S rRNA gene sequence for the 92 selected organisms. Names in green and cyan indicate plant-associated species (green, symbionts; cyan, nonsymbionts). The dimension of the circles is proportional to the genome size, while the color of the circles indicates the GC content.

Mentions: First a dataset of the relevant Alphaproteobacteria (“alphas” for short) was constructed by downloading all the alphaproteobacterial genomes available in NCBI genome database. All animal obligate pathogens were excluded, since they show extensive genome reductions, linked with intracellular lifestyle [4,19], as well as the SAR11 clade due to the extensive gene loss described for this group [1]. A total of 92 genomes were then analyzed (Figure 1 and Supplementary Material S1), and divided into three groups: (i) solely free-living, (ii) plant-associated and (iii) symbiont (that is a sub-set of plant-associated) combining the information available on GOLD database [20,21], Bergey's manual of systematic bacteriology [22] and bibliographic search on Pubmed. Plant-associated bacteria include 27 genomes (2 pathogens, 7 associated and 18 symbionts), all but two (25/27) grouped within the order Rhizobiales (Figure 1), the only exceptions are the species Gluconacetobacter diazotrophicus and Azospirillum B510 which fall in the order Rhodospirillales; of course we cannot exclude that among the 65 nonplant-associated bacteria some could have also experienced the plant environment, even if those putative events have not been reported.


Plant-bacteria association and symbiosis: are there common genomic traits in alphaproteobacteria?

Pini F, Galardini M, Bazzicalupo M, Mengoni A - Genes (Basel) (2011)

Phylogenetic tree based on 16S rRNA gene sequence for the 92 selected organisms. Names in green and cyan indicate plant-associated species (green, symbionts; cyan, nonsymbionts). The dimension of the circles is proportional to the genome size, while the color of the circles indicates the GC content.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3927591&req=5

f1-genes-02-01017: Phylogenetic tree based on 16S rRNA gene sequence for the 92 selected organisms. Names in green and cyan indicate plant-associated species (green, symbionts; cyan, nonsymbionts). The dimension of the circles is proportional to the genome size, while the color of the circles indicates the GC content.
Mentions: First a dataset of the relevant Alphaproteobacteria (“alphas” for short) was constructed by downloading all the alphaproteobacterial genomes available in NCBI genome database. All animal obligate pathogens were excluded, since they show extensive genome reductions, linked with intracellular lifestyle [4,19], as well as the SAR11 clade due to the extensive gene loss described for this group [1]. A total of 92 genomes were then analyzed (Figure 1 and Supplementary Material S1), and divided into three groups: (i) solely free-living, (ii) plant-associated and (iii) symbiont (that is a sub-set of plant-associated) combining the information available on GOLD database [20,21], Bergey's manual of systematic bacteriology [22] and bibliographic search on Pubmed. Plant-associated bacteria include 27 genomes (2 pathogens, 7 associated and 18 symbionts), all but two (25/27) grouped within the order Rhizobiales (Figure 1), the only exceptions are the species Gluconacetobacter diazotrophicus and Azospirillum B510 which fall in the order Rhodospirillales; of course we cannot exclude that among the 65 nonplant-associated bacteria some could have also experienced the plant environment, even if those putative events have not been reported.

Bottom Line: To shed some light on possible common genetic features in such a heterogeneous set of plant associations, the genomes of 92 Alphaproteobacteria strains were analyzed with a fuzzy orthologs-species detection approach.Two of these orthologous groups were also detected in fully sequenced plant-associated Betaproteobacteria and Gammaproteobacteria.Overall these results lead us to hypothesize that plant-bacteria associations, though quite variable, are partially supported by a conserved set of unsuspected gene functions.

View Article: PubMed Central - PubMed

Affiliation: Department of Evolutionary Biology, University of Florence, via Romana 17, 50125 Firenze, Italy. francesco.pini@unifi.it.

ABSTRACT
Alphaproteobacteria show a great versatility in adapting to a broad range of environments and lifestyles, with the association between bacteria and plants as one of the most intriguing, spanning from relatively unspecific nonsymbiotic association (as rhizospheric or endophytic strains) to the highly species-specific interaction of rhizobia. To shed some light on possible common genetic features in such a heterogeneous set of plant associations, the genomes of 92 Alphaproteobacteria strains were analyzed with a fuzzy orthologs-species detection approach. This showed that the different habitats and lifestyles of plant-associated bacteria (soil, plant colonizers, symbiont) are partially reflected by the trend to have larger genomes with respect to nonplant-associated species. A relatively large set of genes specific to symbiotic bacteria (73 orthologous groups) was found, with a remarkable presence of regulators, sugar transporters, metabolic enzymes, nodulation genes and several genes with unknown function that could be good candidates for further characterization. Interestingly, 15 orthologous groupspresent in all plant-associated bacteria (symbiotic and nonsymbiotic), but absent in nonplant-associated bacteria, were also found, whose functions were mainly related to regulation of gene expression and electron transport. Two of these orthologous groups were also detected in fully sequenced plant-associated Betaproteobacteria and Gammaproteobacteria. Overall these results lead us to hypothesize that plant-bacteria associations, though quite variable, are partially supported by a conserved set of unsuspected gene functions.

No MeSH data available.