Leaf Nodule Development in Psychotria kirkii Hiern. (Rubiaceae)

Miller, I. M.; Scott, A.; Gardner, I. C.

doi:10.1093/oxfordjournals.aob.a086638

Cited by 22 publications

(18 citation statements)

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“…3). This is consistent with the observations of Miller and colleagues, who speculated that the invasion of the newly formed substomatal chamber leading to the developing nodule is a passive process occurring exclusively in the shoot tip (Miller et al, 1983;Miller, 1990). These COG categories include many essential housekeeping genes involved in basic processes within the cell and may therefore be less likely to accumulate debilitating mutations.…”

Section: Comparative Genomics and Evidence Of Genome Erosionsupporting

confidence: 91%

“…However, close inspection showed that virtually all the amino acid utilization pathways are inexistent or non-functional, while the pathways for amino acid biosynthesis are conserved, with the notable exception of the Met biosynthetic pathway (Table S4). We also suspect that the large 'lipid droplets' seen by Miller and colleagues in the mature B. kirkii cells may be PHB granules (Miller et al, 1983). Together, these observations suggest that the nitrogen available to B. kirkii for primary metabolism is scarce.…”

Section: Nitrogen Metabolismmentioning

confidence: 70%

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The eroded genome of a Psychotria leaf symbiont: hypotheses about lifestyle and interactions with its plant host

Carlier

Eberl

2012

Environmental Microbiology

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Several plant species of the genus Psychotria (Rubiaceae) harbour Burkholderia sp. bacteria within specialized leaf nodules. The bacteria are transmitted vertically between plant generations and have not yet been cultured outside of their host. This symbiosis is also generally described as obligatory because plants devoid of symbionts fail to develop into mature individuals. We sequenced for the first time the genome of the symbiont of Psychotria kirkii in order to shed some light on the nature of their symbiotic relationship. We found that the 4 Mb genome of Candidatus Burkholderia kirkii (B. kirkii) is small for a Burkholderia species and displays features consistent with ongoing genome erosion such as large proportions of pseudogenes and transposable elements. Reductive genome evolution affected a wide array of functional categories that may hinder the ability of the symbiont to be free-living. The genome does not encode functions commonly found in plant symbionts such as nitrogen fixation or plant hormone metabolism. Instead, a collection of genes for secondary metabolites' synthesis is located on the 140 kb plasmid of B. kirkii and suggests that leaf nodule symbiosis benefits the host by providing protection against herbivores or pathogens.

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Section: Comparative Genomics and Evidence Of Genome Erosionsupporting

confidence: 91%

Section: Nitrogen Metabolismmentioning

confidence: 70%

The eroded genome of a Psychotria leaf symbiont: hypotheses about lifestyle and interactions with its plant host

Carlier

Eberl

2012

Environmental Microbiology

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“…The earliest isolation of a nodule-inducing methylotroph from a plant was of Mycoplana rubra (now Mtb extorquens strain RP4, NCIMB 10409) from surface-sterilized leaf nodules of the Zimbabwean evergreen tree, Psychotria mucronata (Rubiaceae; now P. kirkii), by M. E. Rhodes-Roberts (cited by Green 2006;Miller et al 1983). Several reports have demonstrated that Methylobacterium species could be isolated from root nodules of some leguminous plants (Jaftha et al 2002;Sy et al 2001a, b), and a study of a homogeneous group of 72…”

Section: Methylobacterium and Plantsmentioning

confidence: 99%

The Family Methylobacteriaceae

Kelly¹,

McDonald²,

Wood³

2014

The Prokaryotes

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“…In both cases the uncultured microbes are highly enriched in association with their hosts, making it feasible to construct an ideal metagenomic library containing sufficient copies of interesting genomes from the uncultured microbes. In a few plants, microbes are also found inhabiting particular sites, such as the root nodules of legumes (Bauer 1981) and leaf galls (Miller et al 1983). For most plants, however, little is known about the diversity and colonization sites of microbes, so metagenomic libraries contain a high proportion of plant genomic DNA.…”

Section: Introductionmentioning

confidence: 99%

Enrichment for microbes living in association with plant tissues

et al. 2006

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Aims: To investigate a cultivation‐independent method of enrichment for microbes living in association with plant tissues. Methods and Results: A large quantity of leaves or seeds was enzymatically hydrolyzed, and the pellets were collected by differential centrifugation. Enzyme concentration, buffer and incubation time were optimized for release of plant‐associated microbes. The relative abundance of plant nuclear DNA and bacterial DNA in the enriched sample was estimated by PCR amplification of genome‐specific marker genes. The efficiency of microbe enrichment was estimated from the proportion of bacterium‐derived clones and their restriction fragment length polymorphism (RFLP) types as detected by 16S rRNA gene‐based techniques. With a higher ratio of bacterial to plant nuclear DNA, the enriched samples showed a considerably enhanced proportion of bacterium‐derived clones and a wider sequence diversity of those clones. Conclusions: The method described here proved to be remarkably effective in enriching for bacteria living in association with plant tissues. Significance and Impact of the Study: The method can be applied to study plant‐associated microbes in the field of environmental molecular ecology and environmental metagenomics.

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Leaf Nodule Development in Psychotria kirkii Hiern. (Rubiaceae)

Cited by 22 publications

References 0 publications

The eroded genome of a Psychotria leaf symbiont: hypotheses about lifestyle and interactions with its plant host

The eroded genome of a Psychotria leaf symbiont: hypotheses about lifestyle and interactions with its plant host

The Family Methylobacteriaceae

Enrichment for microbes living in association with plant tissues

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