Phylogenetic lineages in Vanguerieae (Rubiaceae) associated with Burkholderia bacteria in sub-Saharan Africa

Metagenomics of African Empogona and Tricalysia (Rubiaceae) reveals the presence of leaf endophytes

Background

Leaf symbiosis is a phenomenon in which host plants of Rubiaceae interact with bacterial endophytes within their leaves. To date, it has been found in around 650 species belonging to eight genera in four tribes; however, the true extent in Rubiaceae remains unknown. Our aim is to investigate the possible occurrence of leaf endophytes in the African plant genera Empogona and Tricalysia and, if present, to establish their identity.

Methods

Total DNA was extracted from the leaves of four species of the Coffeeae tribe (Empogona congesta, Tricalysia hensii, T. lasiodelphys, and T. semidecidua) and sequenced. Bacterial reads were filtered out and assembled. Phylogenetic analysis of the endophytes was used to reveal their identity and their relationship with known symbionts.

Results

All four species have non-nodulated leaf endophytes, which are identified as Caballeronia. The endophytes are distinct from each other but related to other nodulated and non-nodulated endophytes. An apparent phylogenetic or geographic pattern appears to be absent in endophytes or host plants. Caballeronia endophytes are present in the leaves of Empogona and Tricalysia, two genera not previously implicated in leaf symbiosis. This interaction is likely to be more widespread, and future discoveries are inevitable.

Identification and Characterisation of Endophytic Bacteria from Coconut (Cocos nucifera) Tissue Culture

The coconut is an important economic crop in the Philippines which currently ranks as the world's second largest producer. This study characterised and identified endophytes from coconut tissue culture in order to gain an initial understanding of their potential uses as sources of bioproducts. The isolates were evaluated using morphological, biochemical and molecular methods. Gram staining results revealed that four out of five bacteria isolated were Gram positive. Isolate CEB 1 fermented all three sugars in the Triple Sugar Iron Test while the other four did not. 16S rDNA gene fragments were amplified from genomic DNA using the universal primers 16F27 and 16R1542. The 16S rDNA sequence were found to be homologous to Bacillus subtilis and Pantoea dispersa. Phylogenetic analyses showed significant clustering of bacterial isolates together with archived DNA of B. subtilis and P. dispersa. All isolated bacteria matched the characteristics of their molecular homologies. Isolate CEB 5, identified as B. subtilis, produced red pigments which are possibly pulcherrimin. Literature reports that pulcherrimin possesses antimicrobial activity against yeast species, microscopic fungi, and postharvest pathogens. P. dispera, on the other hand, has been reported to convert insoluble phosphorus into soluble form to enable plants to take up more phosphorus. Determination of the bioactivities of endophytes reported in this study may enable the discovery of novel bioproducts.

Detection of Burkholderia in the seeds of Psychotria punctata (Rubiaceae) - Microscopic evidence for vertical transmission in the leaf nodule symbiosis

Background and aims

The bacterial leaf nodule symbiosis is a close interaction between endophytes and their plant hosts, mainly within the coffee family. The interaction between Rubiaceae species and Burkholderia bacteria is unique due to its obligate nature, high specificity, and predominantly vertical transmission of the endophytes to the next generation of host plants. This vertical transmission is intriguing since it is the basis for the uniqueness of the symbiosis. However, unequivocal evidence of the location of the endophytes in the seeds is lacking. The aim of this paper is therefore to demonstrate the presence of the host specific endophyte in the seeds of Psychotria punctata and confirm its precise location. In addition, the suggested location of the endophyte in other parts of the host plant is investigated.

Methods

To identify and locate the endophyte in Psychotria punctata, a two-level approach was adopted using both a molecular screening method and fluorescent in situ hybridisation microscopy.

Key results

The endophytes, molecularly identified as Candidatus Burkholderia kirkii, were detected in the leaves, vegetative and flower buds, anthers, gynoecium, embryos, and young twigs. In addition, they were in situ localised in leaves, flowers and shoot apical meristems, and, for the first time, in between the cotyledons of the embryos.

Conclusions

Both independent techniques detected the host specific endophyte in close proximity to the shoot apical meristem of the embryo, which confirms for the first time the exact location of the endophytes in the seeds. This study provides reliable proof that the endophytes are maintained throughout the growth and development of the host plant and are transmitted vertically to the offspring.

Members of the genus Burkholderia: good and bad guys

In the 1990s several biocontrol agents on that contained Burkholderia strains were registered by the United States Environmental Protection Agency (EPA). After risk assessment these products were withdrawn from the market and a moratorium was placed on the registration of Burkholderia-containing products, as these strains may pose a risk to human health. However, over the past few years the number of novel Burkholderia species that exhibit plant-beneficial properties and are normally not isolated from infected patients has increased tremendously. In this commentary we wish to summarize recent efforts that aim at discerning pathogenic from beneficial Burkholderia strains.